Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine

Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine

Paperback(Softcover reprint of the original 1st ed. 2004)

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Product Details

ISBN-13: 9781461346944
Publisher: Springer US
Publication date: 10/21/2012
Edition description: Softcover reprint of the original 1st ed. 2004
Pages: 445
Product dimensions: 6.10(w) x 9.25(h) x 0.04(d)

Table of Contents

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-Transcriptional 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 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. Transcriptome Profiling.- 4. Manipulating the Symbiotic Genome.- 5. Endobacterial Genes.- 6. Conclusions.- Acknowledgments.- References.

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