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Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine - Jan S. Tkacz

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Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine

By: Jan S. Tkacz (Editor), Lene Lange (Editor)

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Hardcover | 4 June 2004

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Hardcover
472 Pages

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23.39 x 15.6 x 2.54

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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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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.

Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine

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Hardcover

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