Physiology and Genetics (eBook)

Series Preface 7
It is Time to Retire 10
Volume Preface 11
Contents 13
Chapter 1: Recent Developments in the Molecular Taxonomy of Fungi 20
I. Introduction 20
II. Non-Fungal Organisms Studied by Mycologists 21
A. Slime Moulds 21
B. Plasmodiophora and Related Species 22
C. Straminipila 23
D. Haptoglossa 24
III. The `Basal Fungi´ 24
A. Microsporidia 24
B. Chytrids 25
C. Zygomycete-Type Fungi 25
D. Glomeromycota 26
IV. Ascomycota 26
A. Taphrinomycotina 26
B. Saccharomycotina 26
C. Pezizomycotina 26
V. Basidiomycota 28
A. Pucciniomycotina 28
B. Ustilaginomycotina 30
C. Agaricomycotina 30
VI. Conclusions 32
References 32
Chapter 2: Sordaria macrospora, a Model System for Fungal Development 35
I. Introduction 35
A. Fungal Organisms as Model Systems for Developmental Biology 35
B. Why Choose Sordaria macrospora? 36
II. Biology 37
A. Life Cycle 37
B. Homothallism 38
III. Phylogeny 40
IV. Mutants and Morphology 40
V. Molecular and Genetic Tools 42
A. Tetrad Analysis 43
B. DNA-Mediated Transformations and Gene Libraries 44
C. Tools for Fluorescence Microscopy 45
D. Functional Genomics 48
VI. Developmental Biology and Components of Signalling Pathways 48
A. Pheromones and Pheromone Receptors 49
B. Heterotrimeric G Proteins 49
C. Adenylyl Cyclase 50
D. Transcription Factors 51
E. Novel Developmental Proteins 52
VII Conclusions 54
References 54
Chapter 3: Inteins - Selfish Elements in Fungal Genomes 58
I. Introduction 58
A. General Characteristics of Inteins 59
B. Protein Splicing MechanismProtein splicing mechanism 61
II. Inteins in Fungi 63
A. VMA1 InteinsVMA1 inteins of Saccharomycete Yeasts 63
B. PRP8 Inteins in Fungi 63
1. Distribution of PRP8 InteinsPRP8 inteins in Fungi 63
2. Activity of Fungal PRP8 Inteins 66
C. Other Fungal Inteins 67
III. Mobility, Evolution, and Domestication of Inteins 69
A. Mobility of Fungal InteinsMobility of fungal inteins 69
B. Evolution of Fungal InteinsEvolution of fungal inteins 70
C. Domestication of Fungal Inteins 71
IV. Application of Inteins 71
A. Inteins and Their Application in Protein-Protein Interactionprotein-protein interaction Studies 71
B. Regulation of Protein-Splicing Activity 72
C. Intein-Mediated Protein Purificationprotein purification 73
D. Screening Systems for Protein-Splicing Inhibitorssplicing inhibitors 73
V. Conclusions 74
References 74
Chapter 4: Apoptosis in Fungal Development and Ageing 79
I. General Description of Apoptosis 79
A. Apoptosis in Mammals 79
B. Apoptosis in Fungi 81
C. Differences Between Fungal and Mammalian Apoptosis 82
II. Apoptosis in Fungal Development 82
A. Apoptosis in Host-Pathogen and Antagonistic Interactions 82
B. Apoptosis During Fungal Reproduction 85
C. The Role of Apoptosis in Fungal Lifespan Control 87
III. Concluding Remarks and Future Directions 89
References 90
Chapter 5: Communication of Fungi on Individual, Species, Kingdom, and Above Kingdom Levels 95
I. Introduction 95
II. Communication Within and Between Fungal Colonies - Vegetative Interactions 96
A. Communication in Mediating Vegetative Fusions Within Fungal Colonies 96
B. Communication in Mediating Vegetative Fusions Between Different Individuals of Filamentous Ascomycetes 97
C. Communication in Mediating Vegetative Fusions Between Different Individuals of Basidiomycetes 97
D. Communication in Population Growth Control and Germination 100
E. Communication in Dimorphism and Asexual Reproduction 102
III. Communication Between Fungi in Sexual Interactions 103
A. Communication in Mating 103
B. Communication in Fruiting Body Development 104
IV. Communication Between Fungi and Bacteria 107
V. Communication Between Fungi and Plants 108
VI. Communication Between Fungi and Animals 109
VII. Conclusions 111
References 113
Chapter 6: Yeast Killer Toxins: Fundamentals and Applications 123
I. Introduction 123
II. Chromosomally Encoded Killer Toxins 123
A. Williopsis 123
B. Pichia 126
C. Kluyveromyces 128
III. Extrachromosomally Encoded Toxins 128
A. dsRNA Virus Toxins 128
1. K1 130
2. K28 131
3. Other dsRNA Virus Toxins 132
B. Linear Plasmid-Encoded Toxins 132
1. Group I 133
2. Group II 135
IV. Applications 136
A. Antifungals for Human Therapy 136
B. Antifungals in Agriculture, Food and Feed Industry 137
C. Killer Toxins in Biotyping 139
V. Concluding Remarks 139
References 140
Chapter 7: Evolutionary and Ecological Interactions of Mould and Insects 147
I. Introduction 147
II. Genetics of Secondary Metabolites in Mycelial Fungi 148
A. Different Types of Fungal Secondary Metabolites 148
1. Alkaloids 148
2. Non-Ribosomal Peptides 148
3. Polyketides 149
4. Terpenes 149
B. Fungal Secondary Metabolite Clusters 149
1. Aflatoxin and Sterigmatocystin Clusters 149
2. Epipolythiodioxopiperazine clusters 151
C. Regulation of Secondary Metabolite Synthesis 151
1. Pathway-Specific Regulation 151
2. Global Regulation 151
3. Regulation by Signal Transduction 154
4. Activation of Silent Secondary Metabolite Clusters 155
III. Three Types of Fungus-Insect Interactions and the Role of Secondary Metabolites 155
A. Host-Pathogen 156
B. Predator-Prey 157
C. Interspecific Competition 159
IV. Melding Ecology and Molecular Biology 162
V. Conclusions 163
References 163
Chapter 8: Endophytic Fungi, Occurrence and Metabolites 168
I. Introduction 169
II. The Ecological Relevance of Endophytic Fungi 169
III. Metabolites Isolated from Host Plants and Their Endophytic Fungi 171
A. Taxol 171
B. Camptothecin 172
C. Ergot Alkaloids 172
D. Mycotoxins in Baccharis Species 172
E. Hypericin 173
F. Podophyllotoxin 173
IV. Metabolites from Endophytic Fungi 174
A. Metabolites from Endophytic Xylariaceous Fungi 174
1. 7-Amino-4-Methylcoumarin from Xylaria sp. of Ginkgo biloba 174
2. Metabolites from Xylaria sp. from Sandoricum koetjape 174
3. Sesquiterpenoids from a Xylariaceous Fungus 178
4. Metabolites from Xylaria sp. 178
B. Metabolites from Endophytic Phomopsis or Diaporthe Species 179
1. Lactones from Phomopsis sp. from Azadirachata indica 179
2. Metabolites from Diaporthe sp. from Camellia sinensis L. 180
3. Metabolites from Phomopsis sp. from Camptotheca acuminata 181
4. Sesquiterpenoids from Phomopsis cassiae from Cassia spectabilis 181
5. Metabolites from Phomopsis spp. from Erythrina crista-galli 181
6. Metabolites from Phomopsis sp. from Eupatorium arnottianum 184
7. Cytosporone D from Phomopsis sp. of Phytolacca dioica 185
8. Xanthone Dimers from Phomopsis sp. from Tectona grandis L. 185
9. Dicerandrols from Phomopsis longicolla from the Mint Dicerandra frutescens 185
C. Metabolites from Endophytic Penicillium Species 185
1. Metabolites from Penicillium sp. from Aegiceras corniculatum L. 185
2. Metabolites from Penicillium chrysogenum from Cistanche deserticola 185
3. Metabolites from Penicillium spp. from Prumnopitys andina 186
4. Penicidones from Penicillium sp. from Quercus variabilis 189
D. Metabolites from Endophytic Alternaria Species 189
1. Metabolites from Alternaria sp. from Polygonum senegalense 189
2. Metabolites from Alternaria spp. from Vinca minor and Euonymus europaeus 190
E. Xanthones from Emericella variecolor from Croton oblongifolius 190
F. Cyclopentenons from Dothideomycete sp. from Leea rubra 190
G. Metabolites from Endophytic Chaetomium Species 191
1. Metabolites from Chaetomium sp. from Nerium oleander L. 191
2. Cytochalasan Alkaloids from Chaetomium globosum from Imperata cylindrica 192
H. Metabolites from Endophytic Pestalotiopsis Species 193
1. Isopestacin from Pestalotiopsis microspora from Terminalia morobensis 193
2. Sesquiterpenes from Pestalotiopsis sp. from Pinus taeda 193
3. Metabolites from Pestalotiopsis foedan 194
4. Metabolites from Pestalotiopsis theae 194
J. Metabolites from Phyllosticta spinarum from Platycladus orientalis 195
K. Metabolites from Endophytic Fusarium Species 196
1. CR377 from Fusarium sp. from Selaginella pallescens 196
2. Lipopeptides from Fusarium sp. from Maackia chinensis 196
L. Epichlicin from Epichloe typhina from Phleum pretense L. 196
M. Metabolite from Colletotrichum dematium from Pteromischum sp. 196
N. Hormonemate from Hormonema dematioides from Pinus sp. 197
O. Brefeldin A from Phoma medicaginis from Medicago lupulina 198
P. Phaeosphaerides from an Endophytic Fungus 198
Q. Metabolites from Nodulisporium sp. from Junipercus cedre 198
R. Metabolites from Ascochyta sp. from Meliotus dentatus 198
S. Metabolites from Endophytic Fungi from Garcinia Species 199
T. Metabolites from Endophytic Fungi from Artemisia species 202
U. Metabolites from Endophytes from Schinus molle 204
V. Conclusion 204
References 204
Chapter 9: Fungal Origin of Ergoline Alkaloids Present in Dicotyledonous Plants (Convolvulaceae) 211
I. The Ecological Role of Natural Products 211
II. The Symbiosis Between Poaceae and Clavicipitaceous Fungi 212
III. Epibiotic Clavicipitaceous Fungi Associated with Convolvulaceae 213
A. Identification of Clavicipitaceous Fungi 213
1. Microscopic and Electron Microscopic Characterization 213
2. Phylogenetic Trees 216
B. Fungicidal Treatment 216
C. Plant Growth Under Germ-Free Conditions 217
D. Biosynthesis and Accumulation of Ergoline Alkaloids in the Fungus/Plant Symbiotum 218
E. Seed Transmittance of Epibiotic Fungi Colonizing Convolvulaceae 218
IV. Additional Fungus/Plant Symbiota in Dicotyledonous Plants 219
V. Conclusions 220
References 220
Chapter 10: Secondary Metabolites of Basidiomycetes 223
I. Introduction 224
II. Secondary Metabolites and Their Biological Activities 224
A. Terpenoids 225
1. Sesquiterpenoids 225
a) Resupinatus leightonii (Tricholomataceae) 225
b) Conocybe siliginea (Bolbitiaceae) 226
c) Ripartites tricholoma and R. metrodii (Paxillaceae) 226
d) Omphalotus olearius, O. nidiformis (Omphalotaceae) 227
e) Radulomyces confluens (Corticiaceae s. lat.) 227
f) Gloeophyllum sp. (Gloephyllaceae) 228
g) Bovista sp. (Lycoperdaceae) 228
h) Marasmius sp. (Tricholomataceae) 228
i) Dichomitus squalens (Polyporaceae) 228
j) Macrocystidia cucumis (Tricholomataceae) 228
k) Creolophus cirrhatus (Hericiaceae) 230
l) Coprinus sp. (Coprinaceae) 230
m) Dacrymyces sp. (Dacrymycetaceae) 230
n) Limacella illinita (Amanitaceae) 231
o) Boletus calopus (Boletaceae) 231
p) Russula lepida (Russulaceae) 231
2. Diterpenoids 231
a) Sarcodon scabrosus (Thelephoraceae) 231
b) Mycena tintinnabulum (Tricholomataceae) 231
3. Triterpenoids 232
a) Irpex sp. (Steccherinaceae) 232
b) Favolaschia spp. (Favolaschiaceae) 232
c) Fomitella fraxinea (Polyporaceae) 233
d) Grifola frondosa (Polyporaceae s. lat.) 233
e) Leucopaxillus gentianeus (Tricholomataceae) 233
f) Clavariadelphus truncatus (Clavariaceae) 234
B. Polyketides, Fatty Acid Derivatives 234
C. Compounds of Unclear Biogenetic Origin 237
HeadingsSec44_10 237
a) Tremella aurantialba (Tremellaceae) 237
b) Stereum hirsutum (Stereaceae) 238
c) Antrodia serialis (Polyporaceae s. lat.) 238
d) Aporpium caryae (Tremellaceae) 238
e) Bondarzewia montana (Bondarzewiaceae) 238
f) Cortinarius sp. (Cortinariaceae) 238
g) Chamonixia pachydermis (Boletaceae) 239
h) Serpula himantoides (Coniophoraceae) 239
i) Pholiota spumosa (Strophariaceae) 239
D. Amino Acid Derivatives 240
III. Conclusions 240
References 242
Chapter 11: Identification of Fungicide Targets in Pathogenic Fungi 246
I. Introduction 246
II. Currently Deployed Fungicides 246
III. What Are the Ideal Attributes of the Fungicides of the Future? 247
IV. The Role of Traditional Screening Approaches Used in Fungicide Development 247
V. Determining the Mode of Action of an Anti-Fungal Compound 248
VI. Genome-Wide Approaches 248
A. Transcriptomics: Microarrays 248
B. Studying Genome-Wide Transcriptional Changes Which Accompany Differentiation 251
C. Cross-Species Comparisons: Comparative Genomic 252
D. Identifying Possible Drug Targets by Comparison of the Transcriptome of Mutant and Wild-Type Cells 252
E. Exploring Drug Resistance Using Transcriptome Analysis: Candida albicans 253
F. MPSS and SAGE 254
G. Transcriptomics: Outlook 255
H. Other `omics´ 255
VII. Conclusions/Outlook 256
References 256
Chapter 12: Helminth Electron Transport Inhibitors Produced by Fungi 259
I. Introduction 259
II. Inhibitors of Complex I 262
III. Inhibitors of Helminth Complex I 263
A. NADH-Fumarate Reductase 263
B. Nafuredin 263
1. Producing Strain and Fermentation 263
2. Structure 264
3. Enzyme Inhibition and Biological Activity 265
4. Nafuredin-gamma and its Analogs 266
C. Paecilaminol 266
D. Verticipyrone 267
E. Ukulactones 269
IV. Inhibitors of Complex II 270
A. Atpenins and Harzianopyridone 270
1. Structures 270
2. Enzyme Inhibition and Biological Activity 273
B. Other Complex II Inhibitors 273
V. Other Electron Transport Inhibitors 274
A. Inhibitors of Complex III 274
B. Inhibitors of Complex V 275
C. Uncouplers 277
VI. Conclusions 278
References 279
Chapter 13: Cyclic Peptides and Depsipeptides from Fungi 284
I. Introduction 284
II. Occurrence of Cyclic Peptides and Depsipeptides Within the Kingdom Eumycota (True Fungi) 285
A. Siderophores 285
B. Diketopiperazines 285
C. Cyclic Peptides 289
D. Cyclic Depsipeptides 293
III. Chemical and Biological Diversity of Cyclic Peptides and Depsipeptides 296
A. Diversity of Building Blocks 296
B. Diversity of Structures 297
C. Diversity of Biological Activities 298
IV. Ecological Role of Cyclic Peptides and Depsipeptides 300
V. Conclusions 301
References 301
Chapter 14: Fungal Genome Mining and Activation of Silent Gene Clusters 308
I. Introduction 308
II. Fungal Genome Miningand Activation of SilentGene Clusters 308
A. Genetic Potential for Secondary Metabolism Biosynthesis of Fungi 308
B. Genome Mining 309
C. Activation of Silent Gene Clusters 310
III. Conclusions 313
References 313
Chapter 15: Non-Ribosomal Peptide Synthetases of Fungi 315
I. Introduction 315
II. Non-Ribosomal Peptide Synthetases 316
A. Structure of NRPSs 316
B. Module Arrangement 317
C. Domain Types of Non-Ribosomal Peptide Synthetases 319
1. Adenylation Domain 319
a) Functions of Adenylation Domains 319
b) Substrate Specificity 320
2. Thiolation Domains and 4-Phosphopantetheine Transferases 321
3. Condensation Domains 323
4. Modifying Domains 323
a) n-Methylation Domain 324
b) Epimerization Domains and Amino Acid Racemases 324
5. Termination Domains 325
a) Thioesterase Domain 325
b) Reductase Domain 325
c) Condensation Domain 325
III. Distinctions Between Fungal and Bacterial NRPSs 325
IV. Non-Ribosomal Peptide Synthesis in Basidiomycetes 327
V. Physiological Significance of Peptides 328
VI. Examples for NRPS Gene Clusters and Cluster Evolution 329
A. Penicillin and Cephalosporin Biosynthesis 330
B. Ergot Alkaloid Biosynthetic Gene Clusters 331
VII. Conclusions 333
A. Approaches to Identify New NRPSs 333
B. Combinatorial Biosynthesis of New NRPs 334
References 334
Chapter 16: Biosynthesis of Fungal Polyketides 341
I. Introduction 341
II. Ecological Importance and Pharmaceutical Use of Fungal Polyketides 341
III. Biosynthesis of Polyketides 343
IV. Fungal Polyketide Synthase Classes 344
A. Non-Reducing PKS 345
B. Partially Reducing PKS 347
C. Highly Reducing PKS 347
D. Polyketide Synthase-Non-Ribosomal Peptide Synthetase Hybrids 349
V. Post-PKS Modifications 351
VI. Phylogeny 352
VII. Functional Analysis and Engineering of Fungal Polyketide Biosynthesis 354
A. Inactivation of PKS Genes 355
1. Knockout 355
2. Knockdown 356
B. Heterologous Expression of PKS Genes 356
C. PKS Pathway Regulation 357
VIII. Conclusions 357
References 358
Chapter 17: Physiological and Molecular Aspects of Ochratoxin A Biosynthesis 362
I. Introduction 362
II. Ochratoxin A-Producing Fungal Species 362
III. Structure and Biosynthesis of Ochratoxin A 364
IV. Physiological Conditions for Production and Occurrence of Ochratoxin A 366
V. Molecular Biology of Ochratoxin A Biosynthesis 369
VI. Regulation of Expression of Ochratoxin A Biosynthesis Genes in Penicillium in Relation to Environmental Factors 372
VII. Regulation of Ochratoxin A Biosynthesis in Penicillium in Relation to Light 377
VIII. Conclusions 380
References 382
Chapter 18: Genetic and Metabolic Engineering in Filamentous Fungi 386
I. Introduction 386
II. Fungal Genomics: Advances in Exploring Sequence Data 387
III. Post-Genomic Approaches to Unravel the Metabolism of Filamentous Fungi 388
A. Transcriptomics 389
B. Proteomics 389
C. Metabolomics 390
IV. Metabolic Engineering: Finding the Optimum Genetic Strategy 390
A. Choosing the Right Transformation Technique 391
V. Enhancing Gene-Targeting Efficiency 392
A. RNA-Based Tools for Metabolic Engineering 392
VI. Concluding Remarks and Prospects 395
References 395
Chapter : Biosystematic Index 402