| Preface | p. xix |
| Genetic Technology | |
| Practical Molecular Taxonomy of Fungi | |
| Introduction | p. 3 |
| Identifying a Fungus to Species--What does it Mean? | p. 3 |
| Useful Species Definitions | p. 3 |
| Genealogical Concordance as a Means to Recognize Fungal Species | p. 4 |
| Molecular Taxonomy in Practice | p. 6 |
| How do I Identify an Unknown Fungus? | p. 6 |
| The Molecular Toolbox | p. 7 |
| Using the Toolbox | p. 11 |
| What is Next? | p. 12 |
| References | p. 13 |
| Genomics of Filamentous Fungi | |
| Introduction | p. 15 |
| Genomic Projects Focusing on Fungi | p. 16 |
| Genome Structure | p. 18 |
| Gene Identification and Annotation | p. 19 |
| Gene Complement of a Filamentous Fungus | p. 21 |
| Novel Aspects of Fungal Biology | p. 26 |
| Summary | p. 27 |
| References | p. 27 |
| A Molecular Tool Kit for Fungal Biotechnology | |
| Introduction | p. 31 |
| Vectors and Transformation | p. 32 |
| Gene Cloning Tools for Genomic Approaches | p. 32 |
| Fungal Transposons as Tools | p. 33 |
| Tools for Identifying Essential Genes | p. 34 |
| Generating Conditional Lethal Mutants | p. 34 |
| Inference | p. 34 |
| Using Controllable Promoters | p. 34 |
| Post-Transcriptional Gene Silencing (PTGS) | p. 35 |
| Genome-Based Tools | p. 35 |
| Genome-Wide Insertional Mutagenesis | p. 36 |
| Genome-Shuffling | p. 36 |
| Summary | p. 37 |
| References | p. 37 |
| Transformation Mediated by Agrobacterium tumefaciens | |
| Introduction | p. 41 |
| Agrobacterium | p. 42 |
| Host Range | p. 44 |
| T-DNA Transfer Resembles Bacterial Conjugation | p. 44 |
| Accessory Functions Enabling Trans-Kingdom DNA Transfer | p. 49 |
| Protein Translocation from Agrobacterium into Host Cells | p. 50 |
| T-DNA Integration | p. 51 |
| Agrobacterium-Based Vector Systems | p. 52 |
| Transformation of Yeasts and Filamentous Fungi | p. 54 |
| Concluding Remarks | p. 57 |
| References | p. 58 |
| Special (Secondary) Metabolism | |
| Fungal Polyketide Synthases in the Information Age | |
| Introduction | p. 69 |
| Secondary Metabolites | p. 69 |
| Polyketides | p. 71 |
| Types of Polyketide Synthase | p. 72 |
| Non-Fungal PKS | p. 73 |
| Fungal PKS | p. 75 |
| 6-Methylsalicyclic Acid Synthase | p. 76 |
| Fungal PKS Involved in Biosynthesis of Conidial Pigment and Melanin | p. 77 |
| Fungal Polyketide Mycotoxins--Norsolorinic Acid Synthase (NAS) | p. 78 |
| Polyketide Synthase in T-Toxin Production | p. 79 |
| Polyketide Synthase in Fumonisin Production | p. 79 |
| Lovastatin Synthases | p. 80 |
| Novel Methods for Accessing PKS Genes | p. 81 |
| Problems Associated with Cloning Fungal PKS Genes | p. 81 |
| Early Efforts to Develop Fungal PKS Probes | p. 82 |
| Assessing Biosynthetic Potential | p. 85 |
| Biosynthetically Informed Approaches for Accessing Fungal PKS Genes | p. 88 |
| The Genomic Era | p. 92 |
| References | p. 93 |
| More Functions for Multifunctional Polyketide Synthases | |
| Introduction | p. 97 |
| Architecture and Functions of Fungal Polyketide Synthases | p. 100 |
| MSAS/OAS Polyketide Synthases | p. 100 |
| Polyketide Synthases for Aromatic Multi-Ring Products (AR-PKSs) | p. 100 |
| Polyketide Synthases for Reduced Products (RD-PKSs) | p. 103 |
| More Functions for Fungal Polyketide Synthases | p. 106 |
| Claisen Cyclase Domain in AR-PKSs | p. 107 |
| More Functions for AR-PKSs | p. 110 |
| C-Methyltransferase Domains in RD-PKSs | p. 113 |
| PSED (Peptide Synthetase Elongation Domain)-Like Domains in RD-PKSs | p. 114 |
| "Diels-Alderase" in RD-PKSs | p. 115 |
| Concluding Remarks | p. 118 |
| Acknowledgments | p. 120 |
| References | p. 120 |
| Peptide Synthesis Without Ribosomes | |
| Introduction | p. 127 |
| Overview of Non-Ribosomal Peptide Synthetases | p. 129 |
| The "Non-Ribosomal Code" for Fungal NRP Synthetases | p. 132 |
| Parsing Fungal NRP Synthetases | p. 136 |
| Guideline 1 | p. 136 |
| Guideline 2 | p. 137 |
| Guideline 3 | p. 137 |
| Strategies to Identify NRP Synthetases and Genes | p. 138 |
| Tailoring Enzymes and Auxiliary Domains | p. 139 |
| N-Methylation | p. 139 |
| Epimerization | p. 140 |
| Other Tailoring Reactions of Fungal NRP Synthetases | p. 140 |
| Pantetheinylation | p. 141 |
| Regulation | p. 142 |
| Status of Research on Selected Fungal Systems | p. 143 |
| AM-Toxin | p. 143 |
| Cyclosporin | p. 144 |
| Destruxins | p. 145 |
| Enniatins | p. 145 |
| Ergopeptines | p. 146 |
| HC-Toxin | p. 148 |
| Penicillin and Cephalosporin | p. 149 |
| Peptaibols | p. 150 |
| Evolution of NRPs and NRP Synthetases | p. 151 |
| Clustering | p. 151 |
| Evolution of Secondary Metabolite Pathways | p. 152 |
| NRP Synthetases in the Genomics Age | p. 154 |
| Acknowledgments | p. 154 |
| References | p. 155 |
| Isoprenoids: Gene Clusters and Chemical Puzzles | |
| Introduction | p. 163 |
| Sesquiterpenes | p. 165 |
| Trichothecenes | p. 165 |
| Aristolochenes | p. 173 |
| Diterpenes | p. 174 |
| Gibberellins | p. 174 |
| Indole-Diterpenes | p. 179 |
| Tetraterpenes | p. 184 |
| Carotenoids | p. 184 |
| Proteins of Isoprenoid Biosynthetic Pathways | p. 189 |
| Initiation of Prenyl Transfer | p. 189 |
| Prenyl Transferase Structure and Classification | p. 190 |
| Trichodiene Synthase | p. 191 |
| Aristolochene Synthase | p. 192 |
| Final Remarks | p. 192 |
| Acknowledgments | p. 193 |
| References | p. 193 |
| Enzymes and Green Chemistry | |
| Heterologous Expression and Protein Secretion in Filamentous Fungi | |
| Introduction | p. 201 |
| The Past Decade | p. 202 |
| Development of a New Fungal Expression Host: Fusarium venenatum Nirenberg | p. 208 |
| Selection Criteria | p. 208 |
| Heterologous Expression | p. 209 |
| Improved Morphological Mutants | p. 209 |
| Selectable Markers | p. 209 |
| Targeted Gene Deletions | p. 210 |
| GRAS Status for the First Heterologous Enzyme Produced in F. venenatum | p. 210 |
| The First Commercial Recombinant F. venenatum Product | p. 210 |
| Fusarium venenatum Genomics | p. 210 |
| "To Infinity and Beyond" | p. 211 |
| Conclusions | p. 212 |
| References | p. 213 |
| Artificial Evolution of Fungal Proteins | |
| Introduction | p. 221 |
| Artificial Evolution in General | p. 221 |
| Idea Generation | p. 221 |
| In Vitro Generation of Gene Variants | p. 222 |
| In Vitro Mutagenesis and Expression of Fungal Proteins | p. 222 |
| Characterization of Protein Variants Expressed in Yeast | p. 222 |
| Characterization of Protein Variants Expressed in Filamentous Fungi | p. 224 |
| Library Generation in Filamentous Fungi | p. 225 |
| In Vivo Mutagenesis in Fungi | p. 226 |
| In Vivo Shuffling in Yeast | p. 226 |
| In Vivo Shuffling in Neurospora | p. 226 |
| In Vivo Mutagenesis with the RIP System | p. 228 |
| In Vivo Mutagenesis with the Mismatch Repair System | p. 228 |
| Future in Artificial Evolution of Fungal Proteins | p. 231 |
| References | p. 232 |
| Biocatalysis and Biotransformation | |
| Preface | p. 237 |
| Fungal Enzymes and Biotransformations--An Introduction | p. 237 |
| Glycosyl Hydrolases | p. 242 |
| Starch Hydrolysis: Amylases and Glucoamylases | p. 244 |
| Cellulose and Cellulases | p. 245 |
| Hydrolysis of Hemicellulose: Xylanases and Mixed-Linked [beta]-Glucanases | p. 246 |
| Cell Wall Lytic Enzymes | p. 249 |
| Phosphorous Mobilization: Phytases | p. 249 |
| Engineering of Improved Functionality in Aspergillus Phytase | p. 252 |
| Lipases (Triacylglycerol Hydrolases, EC 3.1.1.3) | p. 253 |
| Proteases | p. 254 |
| Degradation of Lignocellulose: Ligninolytic Enzymes | p. 255 |
| Lignin Peroxidase and Manganese Peroxidase | p. 256 |
| Laccase | p. 256 |
| Utilization of Aromatic and Aliphatic Compounds and Hydrocarbons | p. 262 |
| Inactivation of Fungal Biocontrol Agents | p. 263 |
| Creosote | p. 263 |
| Pentachlorophenol | p. 264 |
| Inorganic Wood Preservatives | p. 264 |
| Disinfectants and Deodorants | p. 265 |
| Fungicides in Agriculture and Medicine | p. 265 |
| Food Preservatives | p. 265 |
| Biotransformation of Biphenyls by Fungi | p. 266 |
| Biphenyl | p. 266 |
| Polychlorinated Biphenyls | p. 268 |
| Oxidation of Dibenzofurans and Dibenzodioxins | p. 269 |
| Biotransformation of Diphenyl Ethers and Phenoxy Herbicides | p. 272 |
| Dehalogenation of Aromatic Xenobiotics | p. 275 |
| Trends and Future Developments | p. 276 |
| Novel Fungal Enzymes: Screening, Development, and Specific Features | p. 277 |
| Screening of Fungi Producing Improved Phytases | p. 278 |
| Diversity of Microbial Enzymes Catalyzing Stereoselective Reactions | p. 279 |
| Lactonase in D-Pantothenic Acid Production | p. 279 |
| Aldehyde Reductase in the Production of Chiral Alcohols | p. 279 |
| Laccase-Catalyzed Heteromolecular Coupling of Molecules | p. 279 |
| Heterologous Expression of Fungal Ligninolytic Enzymes | p. 280 |
| Impact of DNA Recombinant Techniques | p. 280 |
| Expression of Aspergillus Phytase in Transgenic Plants | p. 281 |
| Gene Libraries | p. 282 |
| Biomolecular Engineering | p. 282 |
| Concept of Directed Evolution | p. 283 |
| References | p. 283 |
| Organic Acid Production by Filamentous Fungi | |
| Introduction | p. 307 |
| Commercial Successes: Organic Acids from Filamentous Fungi | p. 308 |
| Citric Acid | p. 309 |
| Gluconic Acid | p. 310 |
| Itaconic Acid | p. 310 |
| L-Lactic Acid | p. 311 |
| Market Prospects | p. 311 |
| Biochemistry and Genetics of Organic Acid Production by Filamentous Fungi | p. 312 |
| Aspergillus and Organic Acid Production | p. 312 |
| Rhizopus and Organic Acid Production | p. 325 |
| Final Perspective | p. 332 |
| References | p. 333 |
| Flavors and Fragrances | |
| Introduction | p. 341 |
| Biotransformation of Terpenoids by Fungi | p. 343 |
| Biosynthesis of Terpenyl Esters | p. 348 |
| Generation of Aromatic Flavor Compounds | p. 349 |
| Flavor Compounds from Other Chemical Classes | p. 353 |
| Bioprocess Technology | p. 353 |
| Conclusion | p. 355 |
| References | p. 355 |
| Host-Fungal Interactions | |
| Human Mycoses: The Role of Molecular Biology | |
| Introduction | p. 361 |
| Goals in the Study of Pathogenic Filamentous Fungi | p. 362 |
| Identification of Virulence Factors | p. 362 |
| Identification of Other Drug Targets | p. 362 |
| The Genus Aspergillus | p. 362 |
| Aspergillosis: Spectrum of Disease | p. 363 |
| Aspergilloma | p. 363 |
| Invasive Aspergillosis (IA) | p. 363 |
| Molecular Techniques for the Study of Aspergillus sp. | p. 366 |
| The Agents of Mucormycosis | p. 375 |
| Molecular Techniques for the Study of Mucormycosis | p. 376 |
| Other Pathogenic Filamentous Fungi | p. 379 |
| Future Directions | p. 379 |
| References | p. 379 |
| Molecular Interactions of Phytopathogens and Hosts | |
| Introduction | p. 385 |
| The Life Cycles of Magnaporthe grisea and Ustilago maydis | p. 386 |
| Pathogenicity Factors | p. 387 |
| Regulators of Infection | p. 387 |
| Pathogen-Specific Molecules | p. 394 |
| Plant Recognition Evasion | p. 395 |
| Proteins of Unknown Function | p. 396 |
| Pathogen Associated Molecular Patterns | p. 397 |
| Genomics of Phytopathogens | p. 399 |
| Future Prospects | p. 400 |
| References | p. 400 |
| Structural and Functional Genomics of Symbiotic Arbuscular Mycorrhizal Fungi | |
| Introduction | p. 405 |
| Genome Structure and Organization | p. 407 |
| Fungal Genes in the Symbiotic Context | p. 408 |
| Targeted Analyses of Gene Expression | p. 408 |
| Transcriptome Profiling | p. 412 |
| Manipulating the Symbiotic Genome | p. 414 |
| Endobacterial Genes | p. 417 |
| Conclusions | p. 418 |
| Acknowledgments | p. 419 |
| References | p. 419 |
| Index | p. 425 |
| Table of Contents provided by Rittenhouse. All Rights Reserved. |
