Handbook of fungal biotechnology, Volume 20

Handbook of Fungal Biotechnology Second Edition, Revised and Expaned......Page 1
Preface......Page 4
Contents......Page 6
Contributors......Page 9
2.1 Composition......Page 13
Table of Contents......Page 0
3 THE PLASMA MEMBRANE......Page 14
5 THE CYTOSKELETON......Page 15
6 REGULATION OF ELONGATION/BRANCHING......Page 16
7.3 High-Throughput Analyses (The \"X-omics\" Age)......Page 18
REFERENCES......Page 19
2 HISTORICAL PERSPECTIVE......Page 21
3.1 The Fungal Cell Wall and Digestive Enzymes......Page 22
4 PROTOPLAST REGENERATION......Page 23
6 THE PARASEXUAL CYCLE AND PROTPLAST FUSION CONNECTION......Page 24
8.1 Vegetative Incompatibility and Related Phenomena......Page 26
8.2.2 Aspergillus......Page 28
8.2.5 Trichoderma......Page 29
9 CYTOPLASMIC INFLUENCES IN PROTOPLAST FUSIONS......Page 30
10 CONCLUDING REMARKS......Page 31
REFERENCES......Page 32
2.1 Global Positive-Acting Nitrogen Pathway Regulators......Page 37
2.2 Repressors Involved in Nitrogen Metabolite Repression......Page 38
2.3.3 The meaB Gene Of Aspergillus nidulans......Page 39
3.2.1 CreA, a DNA-Binding Transcriptional Repressor......Page 40
3.2.3 Aspergillus nidulans CreB and CreC Are Involved in Deubiquitination and CCR......Page 41
3.2.5 How Does CreA Effect Repression?......Page 42
4.2 Action of Pathway-Specific Regulators......Page 43
REFERENCES......Page 44
2 A REFLECTION OF TIMES—A PERSONAL ANECDOTE......Page 50
3.1 Nucleolar Structure......Page 51
3.1.1 Nucleolar Subcompartmentalization......Page 52
3.2.1 The Nucleolus May Be a Depot for MRNA Exports from Nucleus to Cytoplasm......Page 53
3.2.3 The Nucleolus May Hold Keys to Cell Cycle and Check Point Controls......Page 54
4 THE SPINDLE POLE BODY......Page 55
4.3 The SPB Plays a Role in MEN Regulation......Page 56
5 THE NUCLEAR PORE COMPLEX (NPC)......Page 57
6.3 Kinetochore Involvement in Spindle Organization......Page 58
7.1 Telomere Capping......Page 59
7.4 Telomeres Play a Role in Homologous Chromosome Pairing in Meiosis......Page 60
REFERENCES......Page 61
2 FILAMENTOUS FUNGI......Page 66
3.1.1 Techniques......Page 67
3.2 Functional Genomics......Page 68
3.2.4 Microarray and Chip Analysis......Page 69
3.3 Computational Genomics Tools......Page 70
4.2 Relevance of Sequencing Data......Page 73
4.3 Relevance of Data Derived from Functional Studies......Page 74
5.2 Metabolomics......Page 75
REFERENCES......Page 76
1 INTRODUCTION......Page 80
2.2.1 Repair Pathways......Page 81
2.2.3 Stress-Induced and Adaptive Mutation......Page 82
2.3.1 Chromosome Disruption by Recombination Between Repeated Sequences......Page 83
3 TELOMERES......Page 84
4.1 Transposon-Induced Damage......Page 85
4.2.1 RIP and MIP......Page 86
REFERENCES......Page 88
2.1 Aflatoxins and Sterigmatocystin......Page 92
2.2 Trichothecenes......Page 94
2.3 Penicillins and Cephalosporins......Page 95
2.5 Fumonisins......Page 96
2.6 Melanins......Page 97
3.2 AK-Toxin......Page 99
4.2 Evolutionary Significance......Page 100
5 CONCLUSIONS......Page 101
REFERENCES......Page 102
2 CLONING STRATEGIES......Page 106
2.1.1 Complementation of Mutants......Page 107
2.2.1 Protein Purification......Page 108
2.4.1 Hybridization-Based Techniques......Page 109
2.5.1 Map-Based Cloning......Page 110
3.2 Recognition Between Plants and Pathogenic Fungi......Page 111
3.4 Genes of Potential Uses in Yeast Improvement......Page 113
3.5 Cloned Fungal Sequences and Improved Heterologous Protein Production......Page 114
3.7 Use of Cloned Genes in Mushroom Improvement......Page 115
REFERENCES......Page 116
2 TRANSFORMATION PROCEDURES FOR FILAMENTOUS FUNGI......Page 120
2.5 Lithium Acetate-Based Transformation......Page 121
3.1 Transformation Vectors......Page 122
3.2 Selectable Markers......Page 123
4.1 Integration of DNA into the Genome......Page 124
5.2 Restriction Enzyme Mediated Integration (REMI)......Page 125
REFERENCES......Page 126
1 INTRODUCTION......Page 131
3.2 Tools for Genetic Analysis......Page 132
4.2 In Vivo Tools......Page 133
5.2 Tools for Genetic Analysis......Page 134
6.2 In Vivo Tools......Page 135
7 CONCLUSIONS......Page 136
REFERENCES......Page 137
2 FUNGAL MITOCHONDRIAL ORIGINS AND FUNCTION......Page 141
3.1 Size and Genetic Exchange......Page 142
3.3 mtDNA Structure......Page 144
3.5 Introns......Page 145
4 MITOCHONDRIAL PLASMIDS......Page 146
5.2 Translational Control......Page 148
6 CONCLUSIONS AND PROSPECTIVE STUDIES......Page 149
REFERENCES......Page 150
2.1 What Are Fungi?......Page 154
2.2 Why Should We Study Fungi?......Page 156
3.1 Why Investigate Fungal Genomes and Gene Expression at the Genome Level?......Page 157
4.2 The Inference of Phylogenies from Sequence Data......Page 158
4.5 Sequence Alignment......Page 159
4.7 Evaluation of the Tree......Page 160
5.2 Phylogeny Based on Nuclear rRNA Sequences......Page 161
5.3 Phylogenies Based on Nuclear-Encoded Protein Sequences......Page 163
5.4 Phylogenies Based on Mitochondrial Protein-Coding Genes......Page 166
ACKNOWLEDGEMENTS......Page 167
REFERENCES......Page 168
2 GENOMIC SEQUENCE PATTERNS......Page 171
2.2 Matrix Attachment Regions......Page 172
3.1.3 Higher Order Markov Models......Page 173
3.2.3 Hidden Markov Models......Page 174
5 MAR DETECTION......Page 175
7 CONCLUSIONS......Page 177
REFERENCES......Page 179
2.2 In Situ Synthesized Oligonucleotide Arrays......Page 180
3 HYBRIDIZATION......Page 182
4.1.1 Total Intensity Normalization......Page 183
4.1.4 Universal Standard......Page 184
7 CONCLUSIONS......Page 185
REFERENCES......Page 186
1 INTRODUCTION......Page 187
3.1 Signaling via Ga Subunits......Page 188
3.2 Gb Subunits and Other Components Involved in G Protein Signaling......Page 189
4 CAMP SIGNALING IN FUNGI......Page 190
5 PATHWAY CROSSTALK......Page 191
6 FUNGAL MITOGEN-ACTIVATED PROTEIN KINASE PATHWAYS......Page 192
8 CONCLUSIONS......Page 194
REFERENCES......Page 195
2 POINTS TO CONSIDER IN STRAIN IMPROVEMENT......Page 199
2.2 Promoters and Secretion Signals......Page 200
2.4 Effect of Steady-State MRNA Levels on Product Yield......Page 201
2.7 Gene Targeting, Multiple Copies, and Knock-Outs......Page 202
3.1 Secretory Pathway at a Glance......Page 203
3.3 ER-Associated Protein Degradation Pathway (ERAD)......Page 204
3.5 Proteolytic Processing in the Secretory Pathway......Page 205
3.6.1 Genes Involved in the Secretion Process......Page 206
4.1 Novel Promoter Strategies......Page 207
REFERENCES......Page 208
2 THE DEVELOMENT OF YEASTS FOR THE IMPROVEMENT OF THE EFFICIENCY OF FERMENTATION......Page 215
2.1 Improved Resilience and Stress Tolerance......Page 216
2.2 Improved Efficiency of Sugar Utilization......Page 217
2.3 Improved Nitrogen Assimilation......Page 218
2.4 Improved Ethanol Tolerance......Page 219
2.5.3 Agrochemicals......Page 220
3.2 Improved Polysaccharide Clarification......Page 221
3.3 Controlled Cell Flocculation and Flotation......Page 222
4 THE DEVELOPMENT OF YEASTS FOR THE IMPROVEMENT OF THE BIOLOGICAL CONTROL OF WINE SPOILAGE......Page 223
4.2.1 Zymocins......Page 224
5 THE DEVELOPMENT OF YEASTS FOR THE IMPROVEMENT OF WINE WHOLESOMENESS......Page 225
5.2 Reduced Formation of Ethyl Carbamate......Page 226
5.3 Reduced Formation of Biogenic Amines......Page 227
6 THE DEVELOPMENT OF YEASTS FOR THE IMPROVEMENT OF WINE FLAVOR AND OTHER SENSORY QUALITIES......Page 228
6.2 Enhanced Production of Desirable Volatile Esters......Page 229
6.4 Enhanced Glycerol Production......Page 230
6.5 Bio-adjustment of Wine Acidity......Page 231
6.7 Reduced Sulfite and Sulfide Production......Page 232
REFERENCES......Page 234
2 GRAIN INTO GOLD: THE INVENTION OF BEER......Page 239
4 YEAST BIODIVERSITY......Page 240
5 HOW DID SACCHAROMYCES YEASTS BECOME GOOD BREWERS?......Page 241
6 METHODOLOGY: HOW TO BREED......Page 242
7.1 Feeding the Beast: Carbohydrate Degradation......Page 243
7.2 Flavor Components: Too Little and Too Much......Page 245
7.3 A Technical Problem: Beer Filtration......Page 246
7.4 Beer Maturation: How to Speed Things Up......Page 248
7.5 Flavor Stability: A Way to Increased Shelf Life......Page 249
REFERENCES......Page 250
2.1.1 Substrates of Potential Use for Ethanol Production......Page 255
2.1.2 Regulation of Substrate Utilization and Ethanol Production......Page 256
2.2.2 Mitochondrial Genome......Page 262
3.1 Improvement of the Environmental Conditions......Page 263
3.2.1 Genetic Features of Industrial Yeasts......Page 264
3.2.3 Efficiency of Substrate Conversion......Page 266
3.2.4 Improvement of Ethanol Production......Page 267
REFERENCES......Page 268
1 INTRODUCTION......Page 272
3.1 Tray Bioreactors......Page 273
5 COMPOSTING/PROTEIN-ENRICHMENT......Page 274
6.3 Surfactin......Page 275
6.9 Iturin......Page 276
REFERENCES......Page 277
2.1 Koji Technology......Page 280
2.4 Moldy Bran......Page 281
3.3 Solid Fermentation with Mechanical Stirring and Aeration......Page 282
4.1.2 Steric Hindrance of Fungal Growth in Porous Supports......Page 283
4.1.3 Effect of Sugar Concentration on the Maximum Biomass Concentration......Page 284
4.1.4 Microscopic Model of Fungal Growth......Page 285
4.2 Macroscopic Limitations of Fungal Growth on Solid Support......Page 286
4.3 Modeling of Enzyme Production Between SSF and SmF Techniques......Page 287
4.4 Comparison of Enzyme Production by SmF and SSF Systems......Page 288
GLOSSARY OF TERMS......Page 289
REFERENCES......Page 290
2 AMYLASES......Page 292
2.1.3 Detergent Industry......Page 293
3.1.5 Other Industrial Uses......Page 294
4.1.6 Medical Industry......Page 295
5.1.1 Bioconversion......Page 296
7 PHYTASE......Page 297
8.1.1 Adsorption of the Enzyme on a Carrier Surface......Page 298
8.6 Immobilization of Xylanase......Page 299
REFERENCES......Page 300
2 PRODUCTION OF XYLANASES......Page 303
4 PURIFICATION OF XYLANASES......Page 306
5.2 Thermal Stability......Page 308
5.5 Substrate Specificity and Mode of Action......Page 309
5.6 Multiplicity of Xylanases......Page 311
6 MOLECULAR STRUCTURE......Page 312
7 APPLICATION POTENTIAL......Page 313
REFERENCES......Page 314
1 INTRODUCTION......Page 318
2.2 Inhibitors of Chitin Synthases......Page 319
2.4 Mechanism of Chitin Synthesis......Page 320
3 CYTOLOGICAL ASPECTS OF CHITIN BIOSYNTHESIS......Page 321
4.2 CHS Gene Multiplicity in Fungi......Page 323
4.3 Phenotypic Alterations in Chs Mutants......Page 324
6 CLASSIFICATION OF CHITIN SYNTHESIS......Page 325
7 EVOLUTION OF CHITIN SYNTHASES......Page 326
8 ON THE STRUCTURE OF THE ACTIVE SITE OF CHITIN SYNTHASE......Page 328
9 CONCLUSIONS......Page 329
REFERENCES......Page 330
2 ISOLATION AND CHARACTERIZATION......Page 334
3 ANTINEOPLASTIC AND IMMUNOSTIMULATING ACTIVITIES......Page 335
5 ROLE IN BIOTECHNOLOGY......Page 338
6 CONCLUSION......Page 339
REFERENCES......Page 340
1 INTRODUCTION......Page 343
2.1.2 Influence of Carbon Sources......Page 344
2.2.2 Culture Conditions......Page 345
3.1 Use of Selected Mutants......Page 346
4.2 Production of Fungal Surfactants......Page 347
5.2 Preparation of Structured Glycerides......Page 348
REFERENCES......Page 349
1 INTRODUCTION......Page 354
2.1 Introduction to the Power-Law Representation......Page 355
3.1 Model Design and Mathematical Representation......Page 356
3.2 Parameter Estimation and Numerical Representation......Page 359
3.4 Robustness......Page 360
4 OPTIMIZATION OF ASPERGILLUS NIGER METABOLISM DURING CRITIC ACID PRODUCTION......Page 362
4.2.2 Constraints......Page 363
4.3 Optimal Solutions......Page 364
5 CONCLUSIONS......Page 365
REFERENCES......Page 366
1 INTRODUCTION......Page 368
2 BIOSYNTHESIS OF FUNGAL CAROTENOIDS......Page 369
3.1 Regulation......Page 370
3.1.2 Mating Type Stimulation......Page 371
3.1.4 Photoregulation......Page 372
3.2 Industrial Production......Page 373
4.2 Industrial Production......Page 374
6 LYCOPENE PRODUCTION......Page 375
REFERENCES......Page 376
1 INTRODUCTION......Page 380
2 ISOPRENOID PATHWAYS......Page 381
3.1 Antifungal Terpenoids......Page 384
3.2 Antibacterial Terpenoids......Page 386
3.4 Antitumor Terpenoid......Page 387
3.5 Other Bioactive Terpenoids......Page 388
4.1 3-Hydroxy-3-Methylglutaryl-Coenzyme A (HMG-CoA) Reductase and Synthase Inhibitors......Page 390
4.2 Squalene Synthase (SQS) Inhibitors......Page 391
4.3 Protein Prenyltransferase Inhibitors......Page 392
4.4 Acyl-CoA:Cholesterol Acyltransferase (ACAT) Inhibitors......Page 393
4.6 Other Modulators of Cholesterol Metabolism......Page 394
5 CONCLUSIONS......Page 395
REFERENCES......Page 396
2.1 Commercial Production of Fungal b-Lactam Anitbiotics: Productivity of Penicillin......Page 401
2.1.3 Selection of Mutants......Page 402
2.1.4 Process Improvement......Page 403
3.1.3 The Last Step in the Penicillin Biosynthesis: Conversion of IPN into Penicillin G......Page 404
3.2 Clustering of Genes for the Biosynthesis of B-Lactam Antibiotics......Page 405
3.3.2 Analysis of the Industrial Strains......Page 406
3.4.1 Carbon Catabolite Regulation......Page 407
3.4.4 Regulation by Glutamate and Glutamine......Page 408
REFERENCES......Page 409
1 INTRODUCTION......Page 412
2.1 General Enzyme Properties......Page 413
2.3 Regulation of Cellulase and Hemicellulase Gene Expression......Page 414
2.4 Industrial Enzyme Applications......Page 415
3.1 Protein Production Strategies......Page 416
3.2 Signalling During Secretion Stress......Page 417
3.3 Glycosylation......Page 418
3.4 Expression of Heterologous Thermophilic Enzymes......Page 419
4.2 Hydrophobin Applications in Protein Production and Purification......Page 420
5 CONCLUSIONS......Page 421
REFERENCES......Page 422
2 BIOTECHNOLOGICAL IMPORTANCE OF THE PLECTOMYCETES......Page 427
3.2.1 Molecular Taxonomy and Chemotaxonomy......Page 430
4.2.2 Onygenales......Page 431
6.1 Conidiogenous Structures and Anamorph-Telemorph Connections......Page 432
6.3 Is Penicillium Really Polyphyletic?......Page 433
7.2 Molecular Clocks and the Time of Plectomycete Divergencies......Page 434
REFERENCES......Page 435
2 THE PRINCIPAL FEATURES OF GFP......Page 439
3 TRANSFORMATION OF FUNGI WITH GFP......Page 440
4 DETECTION TECHNIQUES USED WITH GFP......Page 441
4.3 Confocal Laser Scanning Microscopy......Page 442
6.1 Visualization in Situ......Page 443
6.2 Plant Pathogen Interactions......Page 445
6.3 Interactions Between Fungi......Page 446
REFERENCES......Page 447
1 INTRODUCTION......Page 450
2 ANTIFUNGAL DRUGS—HISTORICAL BACKGROUND......Page 451
3.1 Superficial Fungal Infections......Page 452
3.2 Systemic Fungal Infections......Page 453
4.1 5-Flucytosine (5-FC)......Page 454
4.2 Azoles......Page 455
5.2 Amphotericin B......Page 456
6 FURTHER PROSPECT......Page 457
7 CONCLUSIONS......Page 459
REFERENCES......Page 460
2.1 Ubiquitin-Like Peptides......Page 466
2.4 Lysine Oxidase......Page 467
3 POLYSACCHARIDES AND PROTEIN-BOUND POLYSACCHARIDES......Page 468
4.7 Fungal Toxins......Page 469
5 CONCLUSION......Page 470
REFERENCES......Page 471
1.2 Fungi as Human Pathogens......Page 475
1.4 The Changing Pattern of Fungal Infection......Page 476
1.5 Implications for Diagnosis and Management......Page 477
3 INVASIVE ASPERGILLOSIS AND ITS DIAGNOSIS......Page 478
3.2 Antibody and Antigen Detection......Page 479
3.3 Polymerase Chain Reaction......Page 480
3.5 Clinical and Laboratory Diagnosis of IA in Practice......Page 481
4 SYSTEMIC CANDIDOSIS AND ITS DIAGNOSIS......Page 482
4.5 Combinations of Tests......Page 483
4.7 Comparison of PCR and Culture-Based Methods......Page 484
6 CONCLUSIONS......Page 485
REFERENCES......Page 486
2.4 Other Candida Species......Page 489
5.1 Allergy......Page 490
5.2.2 Mucocutaneous Candidiasis......Page 491
5.2.6 Oesophageal Candidiasis......Page 492
5.2.14 Osteoarticular Candidiasis......Page 493
6.3 Indirect Immunofluorescence......Page 494
8 IMMNOPATHOGENESIS OF CANDIDIASIS......Page 495
9.1 Prevention and Therapy of Candidiasis......Page 496
REFERENCES......Page 497
2.1.1 Deep-Seated Candidiasis......Page 499
2.1.2 Cryptococcosis......Page 500
2.1.4 Systemic Mycoses Caused by Dimorphic Fungi......Page 501
2.2.2 Dermatophytoses......Page 503
3 HUMAN TRIALS......Page 504
4 CONCLUSIONS......Page 505
REFERENCES......Page 506
2 ALLERGIC DISEASES CAUSED BY FUNGI......Page 511
2.4 Allergic Sinusitis......Page 512
3.2 IgE in Antigen Capture and Presentation......Page 513
3.6 Mast Cells......Page 514
4.1 Recombinant Allergens......Page 515
4.1.5 Other Fungi......Page 517
6 IMMUNOTHERAPY AND VACCINATION IN MOLD ALLERGY......Page 518
REFERENCES......Page 519
1.1 The Biological Resource Center......Page 522
2.1.1 The Role of the Modern Biological Resource Center......Page 523
2.1.4 Control of Access Through the Convention on Biological Diversity......Page 524
2.2 Mycological Collections......Page 526
2.3.3 Methodology and Equipment......Page 527
3.2 Freeze-Drying......Page 528
3.3 Cryopreservation......Page 529
3.5 Characterization......Page 530
REFERENCES......Page 532
1 INTRODUCTION......Page 534
3.1 Improving the Processing and Marketing Qualities of Food......Page 535
3.4 Foods with Medicinal Properties......Page 536
4.1 Risk of Producing Allergenic Foods......Page 537
4.3 Risks GM Foods May Pose to Human Populations......Page 538
5.2 Risks Involved with Foods Compared with Pharmaceuticals......Page 539
6.2 Labeling......Page 540
7 CONCLUSIONS......Page 541
REFERENCES......Page 542
1.1 Ecological Needs/Justification for Biotechnology Upgrading Mycoherbicides......Page 544
3 LESSONS FROM THE TRANSGENIC BIOCONTROL OF INSECTS AND DISEASES......Page 545
4.1 The Possible Needs to Upgrade the Crops......Page 546
5 GENES THAT MAY ENHANCE WEED BIOCONTROL......Page 547
5.1.3 Dissolving Host Defenses......Page 548
5.2 Hard Genes Encoding Toxins......Page 549
6.1 Constraints on Using Molecularly-Enhanced Biocontrol Fungi......Page 550
6.2 Is Horizontal Gene Transfer a Risk?......Page 551
7 PREVENTION OF PERSISTENCE AND SPREAD OF TRANSGENIC MYCOHERBICIDES......Page 552
7.1 Obviating Recombination Between Mycoherbicidal Agents and Crop Pathogens......Page 553
8.1 Risk Considerations Based on Pathogen Biology......Page 554
ACKNOWLEDGEMENTS......Page 555
REFERENCES......Page 556
1 INTRODUCTION......Page 560
2 AN INTRODUCTION TO THE CBD......Page 561
3.1 An Introduction to Article 15 of the CBD......Page 562
3.2.1 National Legislation......Page 563
3.2.2 Material Transfer Agreements......Page 564
3.2.4 The Bonn Guidelines on Access and Benefit-sharing......Page 565
4.2 Article 19 of the CBD: The Cartagena Protocol on Biosafety......Page 566
5.1 Access to Samples of Patented Material: The Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure......Page 567
5.2 Disclosure of the Origin of Genetic Resources, and of Prior Informed Consent, in Patient Applications......Page 568
REFERENCES......Page 569