In the past half century, filamentous fungi have grown in commercial importance not only in the food industry but also as sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of specialty proteins and enzymes used to process foods, fortify detergents, and perform biotransformations. The commercial impact of molds is also measured on a negative scale since some of these organisms are significant as pathogens of crop plants, agents of food spoilage, and sources of toxic and carcinogenic compounds. Recent advances in the molecular genetics of filamentous fungi are finding increased application in the pharmaceutical, agricultural, and enzyme industries, and this trend promises to continue as the genomics of fungi is explored and new techniques to speed genetic manipulation become available.
This volume focuses on the filamentous fungi and highlights the advances of the past decade, both in methodology and in the understanding of genomic organization and regulation of gene and pathway expression.
I. Genetic Technology.- 1. Practical Molecular Taxonomy of Fungi.- 1. Introduction.- 2. Identifying a Fungus to Species—What does it Mean?.- 2.1. Useful Species Definitions.- 2.2. Genealogical Concordance as a Means to Recognize Fungal Species.- 2.3. Molecular Taxonomy in Practice.- 3. How do I Identify an Unknown Fungus?.- 3.1 The Molecular Toolbox.- 3.1.1. DNA Sequence Tools.- 3.1.2. Genotyping Methods: Comparing and Identifying Isolates within a Species.- 3.2. Using the Toolbox.- 3.2.1. Tools for Identifying any Fungus.- 3.2.2. Tools for Identifying Fungi in a Particular Taxonomic Group of Intensive Study.- 4. What is Next?.- References.- Genomics of Filamentous Fungi.- 1. Introduction.- 2. Genomic Projects Focusing on Fungi.- 3. Genome Structure.- 4. Gene Identification and Annotation.- 5. Gene Complement of a Filamentous Fungus.- 6. Novel Aspects of Fungal Biology.- 7. Summary.- References.- A Molecular Tool Kit for Fungal Biotechnology.- 1. Introduction.- 2. Vectors and Transformation.- 3. Gene Cloning Tools for Genomic Approaches.- 4. Fungal Transposons as Tools.- 5. Tools for Identifying Essential Genes.- 5.1. Generating Conditional Lethal Mutants.- 5.2. Inference.- 5.3. Using Controllable Promoters.- 5.4. Post-Tranillegalscriptional Gene Silencing (PTGS).- 6. Genome-Based Tools.- 6.1. Genome-Wide Insertional Mutagenesis.- 6.2. Genome-Shuffling.- 7. Summary.- References.- Transformation Mediated by Agrobacterium tumefaciens.- 1. Introduction.- 2. Agrobacterium.- 3. Host Range.- 4. T-DNA Transfer Resembles Bacterial Conjugation.- 5. Accessory Functions Enabling Trans-Kingdom DNA Transfer.- 6. Protein Translocation from Agrobacterium into Host Cells.- 7. T-DNA Integration.- 8. Agrobacterium-Based Vector Systems.- 9. Transformation of Yeasts and Filamentous Fungi.- 10. Concluding Remarks.- 11. References.- II. Special (Secondary) Metabolism.- 5. Fungal Polyketide Synthases in the Information Age.- 1. Introduction.- 1.1. Secondary Metabolites.- 1.2. Polyketides.- 1.3. Types of Polyketide Synthase.- 2. Non-Fungal PKS.- 3. Fungal PKS.- 3.1. 6-Methylsalicyclic Acid Synthase.- 3.2. Fungal PKS Involved in Biosynthesis of Conidial Pigment and Melanin.- 3.3. Fungal Polyketide Mycotoxins—Norsolorinic Acid Synthase (NAS).- 3.4. Polyketide Synthase in T-Toxin Production.- 3.5. Polyketide Synthase in Fumonisin Production.- 3.6. Lovastatin Synthases.- 4. Novel Methods for Accessing PKS Genes.- 4.1. Problems Associated with Cloning Fungal PKS Genes.- 4.2. Early Efforts to Develop Fungal PKS Probes.- 4.3. Assessing Biosynthetic Potential.- 4.3.1. Prokaryotes.- 4.3.2. Lichens.- 4.3.3. Insect and Nematode Associated Fungi.- 4.3.4. Endophytic Fungi.- 4.4 Biosynthetically Informed Approaches for Accessing Fungal PKS Genes.- 4.4.1. KS-Specific Primers.- 4.4.2. KR-Specific Primers.- 4.4.3. CmeT-Specific Primers.- 4.4.4. Lessons and Outlook.- 5. The Genomic Era.- References.- More Functions for Multifunctional Polyketide Synthases.- 1. Introduction.- 2. Architecture and Functions of Fungal Polyketide Synthases.- 2.1. MSAS/OAS Polyketide Synthases.- 2.2. Polyketide Synthases for Aromatic Multi-Ring Products (AR-PKSs).- 2.2.1. Pentaketide 1,3,6,8-Tetrahydroxynaphthalene Synthases.- 2.2.2. Heptaketide Naphthopyrone Synthases.- 2.2.3. PKSs Involved in Aflatoxin Biosynthesis.- 2.3 Polyketide Synthases for Reduced Products (RD-PKSs).- 2.3.1. T-toxin PKS.- 2.3.2. PKSs Involved in Lovastatin Biosynthesis.- 2.3.3. Fumonisin PKS.- 2.3.4. RD-PKS from Alternaría solani.- 3. More Functions for Fungal Polyketide Synthases.- 3.2.1. Claisen Cyclase Domain in AR-PKSs.- 3.2.2. More Functions for AR-PKSs.- 3.2.1. Starter Units.- 3.2.2. N-Termini.- 3.2.3. Interdomain Regions.- 3.2.4. ACP Domains.- 3.3. C-Methyltransferase Domains in RD-PKSs.- 3.4. PSED (Peptide Synthetase Elongation Domain)-Like Domains in RD-PKSs.- 3.5. "Diels-Alderase” in RD-PKSs.- 4. Concluding Remarks.- Acknowledgments.- References.- Peptide Synthesis Without Ribosomes.- 1. Introduction.- 2. Overview of Non-Ribosomal Peptide Synthetases.- 3. The "Non-Ribosomal Code” for Fungal NRP Synthetases.- 4. Parsing Fungal NRP Synthetases.- 4.1. Guidelines 1.- 4.2. Guidelines 2.- 4.3. Guidelines 3.- 5. Strategies to Identify NRP Synthetases and Genes.- 6. Tailoring Enzymes and Auxiliary Domains.- 6.1. N-Methylation.- 6.2. Epimerization.- 6.3. Other Tailoring Reactions of Fungal NRP Synthetases.- 6.4. Pantetheinylation.- 7. Regulation.- 8. Status of Research on Selected Fungal Systems.- 8.1. AM-Toxin.- 8.2. Cyclosporin.- 8.3. Destruxins.- 8.4. Enniatins.- 8.5. Ergopeptines.- 8.6. HC-Toxin.- 8.7. Penicillin and Cephalosporin.- 8.8. Peptaibols.- 9. Evolution of NRPs and NRP Synthetases.- 9.1. Clustering.- 9.2. Evolution of Secondary Metabolite Pathways.- 10. NRP Synthetases in the Genomics Age.- Acknowledgments.- References.- Isoprenoids: Gene Clusters and Chemical Puzzles.- 1. Introduction.- 2. Sesquiterpenes.- 2.1. Trichothecenes.- 2.1.1. Chemical Diversity.- 2.1.2. Gene Clusters.- 2.1.3. Biosynthesis of T2-Toxin.- 2.1.4. Regulation.- 2.2 Aristolochenes.- 3. Diterpenes.- 3.1. Gibberellins.- 3.1.1. Chemical Diversity.- 3.1.2. Gene Cluster.- 3.1.3. Biosynthesis of GA3.- 3.1.4. Regulation.- 3.2 Indole-Diterpenes.- 3.2.1. Chemical Diversity.- 3.2.2. Gene Cluster.- 4. Tetraterpenes.- 4.1. Carotenoids.- 4.1.1. Chemical Diversity.- 4.1.2. Biosynthetic Pathway.- 5. Proteins of Isoprenoid Biosynthetic Pathways.- 5.1. Initiation of Prenyl Transfer.- 5.2. Prenyl Transferase Structure and Classification.- 5.3. Trichodiene Synthase.- 5.4. Aristolochene Synthase.- Final Remarks.- Acknowledgments.- References.- III. Enzymes and Green Chemistry.- Heterologous Expression and Protein Secretion in Filamentous Fungi.- 1. Introduction.- 2. The Past Decade.- 3. Development of a New Fungal Expression Host: Fusarium venenatum Nirenberg.- 3.1. Selection Criteria.- 3.2. Heterologous Expression.- 3.3. Improved Morphological Mutants.- 3.4. Selectable Markers.- 3.5. Targeted Gene Deletions.- 3.6. GRAS Status for the First Heterologous Enzyme Produced in F. venenatum.- 3.7. The First Commercial Recombinant F. venenatum Product.- 3.8. Fusarium venenatum Genomics.- 4. "To Infinity and Beyond”.- 5. Conclusions.- References.- Artificial Evolution of Fungal Proteins.- 1. Introduction.- 2. Artificial Evolution in General.- 2.1. Idea Generation.- 2.2. In Vitro Generation of Gene Variants.- 3. In Vitro Mutagenesis and Expression of Fungal Proteins.- 3.1. Characterization of Protein Variants Expressed in Yeast.- 3.2. Characterization of Protein Variants Expressed in Filamentous Fungi.- 3.3. Library Generation in Filamentous Fungi.- 4. In Vivo Mutagenesis in Fungi.- 4.1. In Vivo Shuffling in Yeast.- 4.2. In Vivo Shuffling in Neurospora.- 4.3. In Vivo Mutagenesis with the RIP System.- 4.4. In Vivo Mutagenesis with the Mismatch Repair System.- 5. Future in Artificial Evolution of Fungal Proteins.- References.- Biocatalysis and Biotransformation.- 1. Preface.- 2. Fungal Enzymes and Biotransformations—An Introduction.- 3.1 Glycosyl Hydrolases.- 3.2 Starch Hydrolysis: Amylases and Glucoamylases.- 3.3 Cellulose and Cellulases.- 3.2.1. Cellulases in Textile and Laundry Biotechnology.- 3.3 Hydrolysis of Hemicellulose: Xylanases and Mixed-Linked ?-Glucanases.- 3.3.1. Xylanases.- 3.3.2. Application: Delignification of Kraft Pulps by Trichoderma Xylanases..- 3.3.3. Mixed Linked ?-Glucan Hydrolyzing Enzymes.- 3.3.4. Application of Cellulases and Hemicellulases in Animal Feed Biotechnology.- 3.4. Cell Wall Lytic Enzymes.- 3.4.1. Macerating Enzymes in Fruit and Vegetable Processing.- 4. Phosphorous Mobilization: Phytases.- 4.1. Engineering of Improved Functionality in Aspergillus Phytase.- 5. Lipases (Triacylglycerol Hydrolases, EC 3.1.1.3).- 6. Proteases.- 7. Degradation of Lignocellulose: Ligninolytic Enzymes.- 7.1. Lignin Peroxidase and Manganese Peroxidase.- 7.2. Laccase.- 7.2.1. Distribution.- 7.2.2. Biological Function of Laccase.- 7.2.3. Isoenzymes.- 7.2.4. Characterization and Some Biochemical Properties.- 7.2.5. Regulation of Laccase Production.- 7.2.6. Laccase Mediator Systems.- 7.2.7. Delignification of Ligninocellulosics by Laccase.- 7.2.8. Purification of Colored Waste Waters.- 7.2.9. Textile Dye Decolorization.- 7.2.10. Transformation and Inactivation of Toxic Environmental Pollutants.- 7.2.11. Beverage and Food Treatment.- 7.2.12. Laccase-Based Biosensors.- 7.2.13. Synthesis of New Chemicals by Laccase.- 7.2.14. Desulfurization and Solubilization of Coal.- 8. Utilization of Aromatic and Aliphatic Compounds and Hydrocarbons.- 9. Inactivation of Fungal Biocontrol Agents.- 9.1. Creosote.- 9.2. Pentachlorophenol.- 9.3. Inorganic Wood Preservatives.- 9.4. Disinfectants and Deodorants.- 9.5. Fungicides in Agriculture and Medicine.- 9.6. Food Preservatives.- 10. Biotransformation of Biphenyls by Fungi.- 10.1. Biphenyl.- 10.2. Polychlorinated Biphenyls.- 11. Oxidation of Dibenzofurans and Dibenzodioxins.- 12. Biotransformation of Diphenyl Ethers and Phenoxy Herbicides.- 13. Dehalogenation of Aromatic Xenobiotics.- 14. Trends and Future Developments.- 14.1. Novel Fungal Enzymes: Screening, Development, and Specific Features.- 14.2. Screening of Fungi Producing Improved Phytases.- 14.3. Diversity of Microbial Enzymes Catalyzing Stereoselective Reactions.- 14.4. Lactonase in D-Pantothenic Acid Production.- 14.5. Aldehyde Reducíase in the Production of Chiral Alcohols.- 14.6. Laccase-Catalyzed Heteromolecular Coupling of Molecules.- 14.7. Heterologous Expression of Fungal Ligninolytic Enzymes.- 14.8. Impact of DNA Recombinant Techniques.- 14.9. Expression of Aspergillus Phytase in Transgenic Plants.- 14.10. Gene Libraries.- 14.11. Biomolecular Engineering.- 14.12. Concept of Directed Evolution.- References.- Organic Acid Production by Filamentous Fungi.- 1.Introduction.- 2.Commercial Successes: Organic Acids from Filamentous Fungi.- 2.1. Citric Acid.- 2.2. Gluconic Acid.- 2.3. Itaconic Acid.- 2.4. L-Lactic Acid.- 2.5. Market Prospects.- 2.6. Biochemistry and Genetics of Organic Acid Production by Filamentous Fungi.- 3.1. Aspergillus and Organic Acid Production.- 3.1.1. Citric Acid.- 3.1.2. Oxalic Acid.- 3.1.3. Gluconic Acid.- 3.1.4. Itaconic Acid.- 3.2. Rhizopus and Organic Acid Production.- 3.2.1. L-Lactic Acid.- 3.2.2. Fumaric Acid.- 3.2.3. L-Malic Acid.- 3.2.4. Succinic Acid.- 3.2.5. (-)-trans-2,3-Epoxysuccinic Acid and meso-Tartaric Acid.- 4. Final Perspective.- References.- Flavors and Fragrances.- 1. Introduction.- 2. Biotransformation of Terpenoids by Fungi.- 3. Biosynthesis of Terpenyl Esters.- 4. Generation of Aromatic Flavor Compounds.- 5. Flavor Compounds from Other Chemical Classes.- 6. Bioprocess Technology.- 7. Conclusion.- References.- IV. Host-Fungal Interactions.- Human Mycoses: The Role of Molecular Biology.- 1. Introduction.- 2. Goals in the Study of Pathogenic Filamentous Fungi.- 2.1. Identification of Virulence Factors.- 2.2. Identification of Other Drug Targets.- 3. The Genus Aspergillus.- 3.1. Aspergillosis: Spectrum of Disease.- 3.2. Aspergilloma.- 3.3. Invasive Aspergillosis (IA).- 3.3.1. Epidemiology and Significance.- 3.3.2. Pathophysiology.- 3.3.3. Virulence Factors of A. fumigatus.- 3.3.4. Clinical Presentation of IA.- 3.3.5. Therapy of IA.- 3.4. Molecular Techniques for the Study of Aspergillus sp.- 3.1.1. Selection Markers for A. fumigatus.- 3.1.2. Transformation Techniques.- 3.1.3. Parasexual Genetics.- 3.1.4. Signature-Tagged Mutagenesis.- 3.1.5. Reporter Gene Systems.- 3.1.6. Transposable Elements in Aspergilli.- 3.1.7. Complementation and Heterologous Expression in Aspergilli.- 3.1.8. Genome Sequencing.- 4. The Agents of Mucormycosis.- 4.1. Molecular Techniques for the Study of Mucormycosis.- 4.1.1. Transformation Techniques.- 4.1.2. Sexual Cycle.- 4.1.3. Heterologous Expression.- 4.1.4. Summary.- 5. Other Pathogenic Filamentous Fungi.- 6. Future Directions.- References.- Molecular Interactions of Phytopathogens and Hosts.- 1. Introduction.- 1.1. The Life Cycles of Magnaporthe grisea and Ustilago maydis.- 2. Pathogenicity Factors.- 2.1. Regulators of Infection.- 2.1.1. The cAMP Response Pathway.- 2.1.2. PMK1 and MAP Kinase Pathways in Fungal Pathogens.- 2.1.3. PMK1 -Related MAP Kinases in Other Phytopathogenic Fungi.- 2.1.4. Alternative MAPK Pathways in M. grisea.- 2.1.5. Nutritional Regulatory Genes.- 2.2. Pathogen-Specific Molecules.- 2.2.1. Toxins and Host-Specific Toxins.- 2.3. Plant Recognition Evasion.- 2.3.1. Saponin Detoxification.- 2.3.2. Phytoalexin Detoxification.- 2.4. Proteins of Unknown Function.- 2.5. Pathogen Associated Molecular Patterns.- 2.5.1. Plant Resistance Mechanisms.- 2.5.2. R Gene and Avr Gene Signaling.- 3. Genomics of Phytopathogens.- 4. Future Prospects.- References.- Structural and Functional Genomics of Symbiotic Arbuscular Mycorrhizal Fungi.- 1. Introduction.- 2. Genome Structure and Organization.- 3. Fungal Genes in the Symbiotic Context.- 3.1. Targeted Analyses of Gene Expression.- 3.2. Tranillegalscriptome Profiling.- 4. Manipulating the Symbiotic Genome.- 5. Endobacterial Genes.- 6. Conclusions.- Acknowledgments.- References.
I. Genetic Technology.- 1. Practical Molecular Taxonomy of Fungi.- Genomics of Filamentous Fungi.- A Molecular Tool Kit for Fungal Biotechnology.- Transformation Mediated by Agrobacterium tumefaciens.- II. Special (Secondary) Metabolism.- 5. Fungal Polyketide Synthases in the Information Age.- More Functions for Multifunctional Polyketide Synthases.- Peptide Synthesis Without Ribosomes.- Isoprenoids: Gene Clusters and Chemical Puzzles.- III. Enzymes and Green Chemistry.- Heterologous Expression and Protein Secretion in Filamentous Fungi.- Artificial Evolution of Fungal Proteins.- Biocatalysis and Biotransformation.- Organic Acid Production by Filamentous Fungi.- Flavors and Fragrances.- IV. Host-Fungal Interactions.- Human Mycoses: The Role of Molecular Biology.- Molecular Interactions of Phytopathogens and Hosts.- Structural and Functional Genomics of Symbiotic Arbuscular Mycorrhizal Fungi.
Inhaltsverzeichnis
I. Genetic Technology.- 1. Practical Molecular Taxonomy of Fungi.- Genomics of Filamentous Fungi.- A Molecular Tool Kit for Fungal Biotechnology.- Transformation Mediated by Agrobacterium tumefaciens.- II. Special (Secondary) Metabolism.- 5. Fungal Polyketide Synthases in the Information Age.- More Functions for Multifunctional Polyketide Synthases.- Peptide Synthesis Without Ribosomes.- Isoprenoids: Gene Clusters and Chemical Puzzles.- III. Enzymes and Green Chemistry.- Heterologous Expression and Protein Secretion in Filamentous Fungi.- Artificial Evolution of Fungal Proteins.- Biocatalysis and Biotransformation.- Organic Acid Production by Filamentous Fungi.- Flavors and Fragrances.- IV. Host-Fungal Interactions.- Human Mycoses: The Role of Molecular Biology.- Molecular Interactions of Phytopathogens and Hosts.- Structural and Functional Genomics of Symbiotic Arbuscular Mycorrhizal Fungi.
Klappentext
In the past half century, filamentous fungi have grown in commercial importance not only in the food industry but also as sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of specialty proteins and enzymes used to process foods, fortify detergents, and perform biotransformations. The commercial impact of molds is also measured on a negative scale since some of these organisms are significant as pathogens of crop plants, agents of food spoilage, and sources of toxic and carcinogenic compounds. Recent advances in the molecular genetics of filamentous fungi are finding increased application in the pharmaceutical, agricultural, and enzyme industries, and this trend promises to continue as the genomics of fungi is explored and new techniques to speed genetic manipulation become available.
This volume focuses on the filamentous fungi and highlights the advances of the past decade, both in methodology and in the understanding of genomic organization and regulation of gene and pathway expression.
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