Handbook of fungal biotechnology, Volume 20 [2nd ed.] 0824740181, 9780824740184
The Handbook of Fungal Biotechnology offers the newest developments from the frontiers of fungal biochemical and molecul
182 56 6MB
English Pages 569 Year 2004
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
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Handbook of Funga I BiotechnoIogy
Second Edition, Revised and Expanded
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edited by
Dilip K. Arora
National Bureau of Agriculturally Important Microorganisms New Delhi, India
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Associate Editors Paul D. Bridge
British Antarctic Survey Cambridge, United Kingdom
Deepak Bhatnagar
U S . Department of Agriculture New Orleans, Louisiana, U.S.A.
MARCEL
MARCELDEKKER, INC. DEKKER
© 2004 by Marcel Dekker, Inc.
NEWYORK BASEL
Although great care has been taken to provide accurate and current information, neither the author(s) nor the publisher, nor anyone else associated with this publication, shall be liable for any loss, damage, or liability directly or indirectly caused or alleged to be caused by this book. The material contained herein is not intended to provide specific advice or recommendations for any specific situation. Trademark notice: Product or corporate names may be trademarks or registered trademarks and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress. ISBN: 0-8247-4018-1 This book is printed on acid-free paper. Headquarters Marcel Dekker, Inc., 270 Madison Avenue, New York, NY 10016, U.S.A. tel: 212-696-9000; fax: 212-685-4540 Distribution and Customer Service Marcel Dekker, Inc., Cimarron Road, Monticello, New York 12701, U.S.A. tel: 800-228-1160; fax: 845-796-1772 Eastern Hemisphere Distribution Marcel Dekker AG, Hutgasse 4, Postfach 812, CH-4001 Basel, Switzerland tel: 41-61-260-6300; fax: 41-61-260-6333 World Wide Web http://www.dekker.com The publisher offers discounts on this book when ordered in bulk quantities. For more information, write to Special Sales/Professional Marketing at the headquarters address above. Copyright q 2004 by Marcel Dekker, Inc. All Rights Reserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any information storage and retrieval system, without permission in writing from the publisher. Current printing (last digit): 10 9 8 7 6 5 4 3 2 1 PRINTED IN THE UNITED STATES OF AMERICA
© 2004 by Marcel Dekker, Inc.
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MYCOLOGY SERIES
Editor
J. W. Bennett Professor Department of Cell and Molecular Biology Tulane University New Orleans, Louisiana Founding Editor
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zyxwvutsrq zy Paul A. Lemke
1. Viruses and Plasmids in Fungi, edited by Paul A. Lemke 2. The Fungal Community: Its Organization and Role in the Ecosystem, edited by Donald T. Wicklow and George C. Carroll 3. Fungi Pathogenic for Humans and Animals (in three parts), edited by Dexter H. Howard 4. Fungal Differentiation:A Contemporary Synthesis, edited by John E. Smith 5. Secondary Metabolism and Differentiation in Fungi, edited by Joan W. Bennett and Alex Ciegler 6. Fungal Protoplasts, edited by John F. Peberdy and Lajos Ferenczy 7. Viruses of Fungi and Simple Eukaryotes, edited by Yigal Koltin and Michael J. Leibowitz 8. Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi, edited by Sally A. Leong and Randy M. Berka 9. The Fungal Community: Its Organization and Role in the Ecosystem, Second Edition, edited by George C. Carroll and Donald T. Wicklow 10. Stress Tolerance of Fungi, edited by D. H. Jennings 11. Metal lons in Fungi, edited by Gunther Winkelmann and Dennis R. Winge 12. Anaerobic Fungi: Biology, Ecology, and Function, edited by Douglas 0. Mountfort and Colin G. Orpin 13. Fungal Genetics: Principles and Practice, edited by Cees J. Bos 14. Fungal Pathogenesis: Principles and Clinical Applications, edited by Richard A. Calderone and Ronald L. Cihlar 15. Molecular Biology of Fungal Development,edited by Heinz D. Osiewacz 16. Pathogenic Fungi in Humans and Animals: Second Edition, edited by Dexter H. Howard 17. Fungi in Ecosystem Processes, John Dighton 18. Genomics of Plants and Fungi, edited by Rolf A. Prade and Hans J. Bohnert 19. Clavicipitalean Fungi: Evolutionary Biology, Chemistry, Biocontrol, and Cultural Impacts, edited by James F. White Jr., Charles W. Bacon, Nigel L. Hywel-Jones, and Joseph W. Spatafora 20. Handbook of Fungal Biotechnology, Second Edition, edited by Dilip K. Arora 21 . Fungal Biotechnology in Agricultural, Food, and EnvironmentalApplications,edited by Dilip K. Arora
Additional Volumes in Preparation
Handbook of lndustrial Mycology, edited by Zhiqiang An
© 2004 by Marcel Dekker, Inc.
Preface
The fungal kingdom comprises one of the most diverse groups of living organisms. They are numerous, ubiquitous, and undertake many roles, both independently and in association with other organisms. The fungal species range from those the size of a few micrometers up to larger fungi with fruiting bodies ranging from several centimeters to meters, and in extreme cases they can develop into a colonial organism that covers many hectares. This diversity of form is also mirrored by functional diversity as fungi can virtually occupy all ecological niches, from slow-growing endolithic communities in the polar regions to highly specialized plant and animal pathogens, and rapid degraders of organic materials in tropical environments. The span of functional diversity in fungi makes them the richest model system in cell biology. Recent developments in molecular biology techniques, including DNA amplification, cloning and expression systems, and modern genomic and proteomic analyses have yielded the discovery of new compounds, and also offered tools to investigate, characterize, and exploit both new and long established fungal activities. Fungi have played a significant role in several biotechnology-based industrial processes and the formulation of a variety of compounds. Fungi are also the target of many biotechnological applications, from the development and production of noteworthy pharmaceuticals and industrial products to their use as systems for homologous and heterologous gene overexpression. The bulk of available literature covers all the major aspects of general mycology, much of which is themed into broad subject areas such as systematics, ecology, biochemistry, pathology, and molecular biology. However, there is a scarcity of compiled literature related strictly to the basic principles of applied mycology and fungal biotechnology. Their broader implications in published literature are fragmented over several specialized journals. In order to attempt to bring together such a diverse field, I, along with coeditors, ventured to edit the five-volume series Handbook of Applied Mycology in 1992. This series offered a comprehensive treatment of basic principles, methods, and applications of mycology as an integrated and multidisciplinary subject. These five volumes presented and collated the major aspects of applied mycology and served as the standard reference for students, teachers, and researchers. Since 1992, significant developments in both biological sciences and industry have broadened the conceptual basis of fungal ecology, physiology, and biochemical processes that are directly relevant to biotechnological usage and manipulation. As a result it seemed timely to revise the original Volume 4 (Fungal Biotechnology) and to review the current developments and highlight advances in rapidly expanding areas of molecular technologies in industry, commercial production technology, and medical biotechnology. The revised second edition of the Handbook of Fungal Biotechnology is intended to provide a broad and detailed introduction to the different aspects of fungal biotechnology, with chapters covering molecular technologies, commercial fungal applications, medical mycology, culture collections, legal aspects, and biosafety. The contributions include both reviews of existing fungal biotechnology applications and details of new processes that may become major applications in the future. For example, new chapters address topics ranging from cell biology of hyphae, protoplast fusion, metabolic regulation pathways, nuclei and chromosomes to genomics, gene clustering, gene cloning and sequencing, fungal mitochondrial genome, fungal genome and evolution, the role of GPF in fungal biotechnology, and DNA chips and
© 2004 by Marcel Dekker, Inc.
microarrays. Coverage has been expanded on commercial applications of fungi, such as the application of genetic engineering for strain improvement, genetic importance of wine yeasts, fungi in brewing, alcohol production, fungal enzymes, role of chitin, polysaccharides, lipids in fungal biotechnology, production of citric acids, caretenoids, terpenoids, antibiotics, antifungal drugs, and antitumor and immunomodulatory compounds. Chapters that have direct or indirect significance in medical biotechnology have also been added. The vast array of usage and properties is testimony to the countless ways in which mankind can harness the benefit of fungi; therefore, characterization techniques and methods of preservations of fungi, the recent development in biotechnology and intellectual property, access to genetic resources, and benefit sharing is essential. These challenging areas of fungal biotechnology are also covered in this book. Potential benefits and dangers of genetically modified foods and mycoherbicides are evaluated. Therefore, the aim of this handbook is to provide a snapshot in time as to the use of fungal biotechnology in different key areas, and to identify potential directions and possibilities for the future. The subject areas related to agriculture, food, and environmental biotechnology are covered not in this volume but in the simultaneously published Fungal Biotechnology in Agricultural, Food, and Environmental Applications from the same editor. In assembling this volume, I have collaborated with world-renowned scientists to illustrate many application areas of fungal biotechnology, from both industry and academia. The contributors are from a broad international background, and thus reflect the diverse activities occurring worldwide. I recognize serious difficulties in developing a comprehensive book on fungal biotechnology because of the range and complexity of the emerging knowledge. However, we have attempted to bring together pertinent information that may serve the needs of the reader, as a quick reference to a subject that might otherwise be difficult to locate, and by furnishing a starting point for further study. I hope that the comprehension of this material by readers will enhance their understanding and help them to gain new appreciation for many potential benefits of fungal biotechnology in a wide variety of fields. The book should be of great interest not only to students, teachers, and researchers but also to agricultural practitioners, mycologists, botanists, microbiologists, molecular biologists, food scientists, biochemists, ecologists, genetic engineers, environmental scientists, pharmacologists, and all those concerned with issues related to significant developments in the field of fungal biotechnology. I am grateful to many colleagues for discussions and their advice during the preparation of this edition, and the academic niche of the Banaras Hindu University for the opportunity to complete this great task. I am grateful to many international authorities and specialists who have graciously consented to share their perspectives and expertise on the diverse applications of fungal biotechnology, and contributed chapters. I am also indebted to Ms. Sandra Beberman, Vice President, Marcel Dekker, Inc., and Ms. Dana Bigelow, Production Editor, for their skill, patience, encouragement, guidance, and support. Dilip K. Arora
© 2004 by Marcel Dekker, Inc.
Contents
Preface Contributors I
CELL BIOLOGY, BIOCHEMICAL AND MOLECULAR TECHNOLOGIES 1
Cell Biology of Hyphae Oded Yarden
2
Protoplast Isolation, Regeneration, and Fusion in Filamentous Fungi Shubha P. Kale and Deepak Bhatnagar
3
Metabolic Pathway Regulation Perng-Kuang Chang and Richard B. Todd
4
Fungal Nuclei and Chromosomes Benjamin C. K. Lu
5
Genomics of Filamentous Fungi: A General Review Ahmad M. Fakhoury and Gary A. Payne
6
Stability and Instability of Fungal Genomes A. John Clutterbuck
7
Secondary Metabolic Gene Clusters in Filamentous Fungi Jeffrey W. Cary
8
Application of Gene Cloning in Fungal Biotechnology Laszlo Hornok and Gabor Giczey
9
Transformation and Gene Manipulation in Filamentous Fungi: An Overview Robert L. Mach
10
Genetic Manipulation Systems for Nonconventional Fungi Johannes W€ostemeyer, Anke Burmester, and Christine Schimek
11
Fungal Mitochondria: Genomes, Genetic Elements, and Gene Expression John C. Kennell and Stephanie M. Cohen
© 2004 by Marcel Dekker, Inc.
12
Fungal Evolution Meets Fungal Genomics Jessica Leigh, Elias Seif, Naiara Rodriguez-Ezpeleta, Yannick Jacob, and B. Franz Lang
13
Genome Sequence Patterns and Gene Regulation: A Bioinformatics Perspective Gautam B. Singh
14
DNA Chips and Microarray Analysis: An Overview Sangdun Choi
15
Signal Transduction in Fungi: Signaling Cascades Regulating Virulence in Filamentous Fungi Susanne Zeilinger
II
COMMERCIAL APPLICATIONS AND BIOTECHNOLOGICAL POTENTIAL
16
Application of Genetic Engineering for Strain Improvement in Filamentous Fungi Helena Nevalainen, Valentino Te’o, and Merja Penttil€a
17
The Genetic Improvement of Wine Yeasts Isak S. Pretorius
18
Fungi in Brewing: Biodiversity and Biotechnology Perspectives Jørgen Hansen and Jure Piskur
19
Ethanol-Tolerance and Production by Yeast Tah´ıa Ben´ıtez and Antonio C. Codon
20
Solid-State Fermentation: An Overview Poonam Nigam, Tim Robinson, and Dalel Singh
21
Basic Principles for the Production of Fungal Enzymes by Solid-State Fermentation Gustavo Viniegra-Gonzalez and Ernesto Favela-Torres
22
Commercial Importance of Some Fungal Enzymes Rajendra K. Saxsena, Bhawana Malhotra, and Anoop Batra
23
Xylanases of Thermophilic Molds and Their Application Potential Seema Rawat and Bhavdish N. Johri
24
Chitin Biosynthesis in Fungi Jose Ruiz-Herrera and Roberto Ruiz-Medrano
25
Bioactive Fungal Polysaccharides and Polysaccharopeptides T. B. Ng
26
Biotechnological Potential of Fungal Lipids Michel Sancholle, Frederic Laruelle, Dorothy M. L€osel, and Jer^ome Muchembled
27
Introduction to the Theory of Metabolic Modeling and Optimization of Biochemical Systems: Application to Citric Acid Production in Aspergillus niger Nestor V. Torres, Fernando Alvarez-Vasquez, and Eberhard O. Voit
28
Fungal Carotenoid Production Javier Avalos and Enrique Cerda-Olmedo
29
Fungal Terpenoid Antibiotics and Enzyme Inhibitors Shigeharu Inouye, Shigeru Abe, and Hideyo Yamaguchi
© 2004 by Marcel Dekker, Inc.
30
Commercial Production and Biosynthesis of Fungal Antibiotics: An Overview S. Gutierrez, R. E. Cardoza, J. Casqueiro, and J. F. Mart´ın
31
Molecular Biology of Trichoderma and Biotechological Applications Merja Pentill€a, Carmen Limon, and Helena Nevalainen
32
Plectomycetes: Biotechnological Importance and Systematics Junta Sugiyama and Hiroyuki Ogawa
33
Exploitation of GFP-Technology with Filamentous Fungi Dan Funck Jensen and Alexander Schulz
III MEDICAL BIOTECHNOLOGY 34
Antifungal Drugs in Fungal Infections Yoshimi Niwano
35
Antitumor and Immunomodulatory Compounds from Fungi T. B. Ng
36
Clinical and Laboratory Diagnosis of Fungal Infections Malcolm Richardson and Simo Nikkari
37
Candidiasis A. G. Palma-Carlos and M. Laura Palma-Carlos
38
Immunizations Against Fungal Diseases in Man and Animals Esther Segal and Daniel Elad
39
Fungal Allergy Viswanath P. Kurup
IV CULTURE COLLECTIONS AND BIOSAFETY 40
Current Status of Fungal Collections and Their Role in Biotechnology David Smith and Matthew J. Ryan
41
Benefits and Risks of Genetically Modified Foods: An Overview Felicity Goodyear-Smith
42
Transgenic Mycoherbicides: Needs and Safety Considerations Jonathan Gressel
43
Recent Developments in Biotechnology and Intellectual Property, Access to Genetic Resources, and Benefit-Sharing Phyllida Cheyne
© 2004 by Marcel Dekker, Inc.
Contributors
Institute of Medical Mycology, Teikyo University, Tokyo, Japan
Shigeru Abe
Fernando Alvarez-Vasquez Universidad de La Laguna, Tenerife, Canary Islands, Spain and Medical University of South Carolina, Charleston, South Carolina, U.S.A. Javier Avalos University of Seville, Seville, Spain Anoop Batra University of Delhi South Campus, New Delhi, India Tahı´a Benı´tez
Universidad de Sevilla, Sevilla, Spain
Deepak Bhatnagar Agricultural Research Service, U.S. Department of Agriculture, New Orleans, Louisiana, USA Anke Burmester
Institut fu¨r Mikrobiologie, Friedrich-Schiller-Universita¨t Jena, Jena, Germany
R. E. Cardoza University of Leo´n, Ponferrada, and INBIOTEC, Leo´n, Spain Jeffrey W. Cary Agricultural Research Service, U.S. Department of Agriculture, New Orleans, Louisiana, USA University of Leo´n, and INBIOTEC, Leo´n, Spain
J. Casqueiro
Enrique Cerda´-Olmedo University of Seville, Seville, Spain Perng-Kuang Chang USA Phyllida Cheyne Sangdun Choi
Agricultural Research Service, U.S. Department of Agriculture, New Orleans, Louisiana,
Barrister-at-law, Geneva, Switzerland California Institute of Technology, Pasadena, California, USA
A. John Clutterbuck
Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland, UK
Antonio C. Codo´n Universidad de Sevilla, Sevilla, Spain Stephanie M. Cohen Daniel Elad
Saint Louis University, St. Louis, Missouri, USA
Kimron Veterinary Institute, Bet Dagan, Israel
© 2004 by Marcel Dekker, Inc.
North Carolina State University, Raleigh, North Carolina, USA
Ahmad M. Fakhoury
Universidad Auto´noma Metropolitana, Iztapalapa, D.F., Me´xico
Ernesto Favela-Torres
Agricultural Biotechnology Center, Go¨do¨llo¨, Hungary
Ga´bor Giczey
Felicity Goodyear-Smith
Weizmann Institute of Science, Rehovot, Israel
Jonathan Gressel S. Gutie´rrez
University of Auckland, Auckland, New Zealand
University of Leo´n, Ponferrada, and INBIOTEC, Leo´n, Spain
Jørgen Hansen
Carlsberg Research Laboratory, Copenhagen-Valby, Denmark
La´szlo´ Hornok Agricultural Biotechnology Center, Go¨do¨llo¨, Hungary Institute of Medical Mycology, Teikyo University, Tokyo, Japan
Shigeharu Inouye
Matthew J. Ryan CABI Bioscience UK Centre, Egham Surrey, United Kingdom Yannick Jacob Canadian Institute for Advanced Research, Universite´ de Montre´al, Montre´al, Que´bec, Canada Dan Funck Jensen The Royal Veterinary and Agricultural University, Copenhagen, Denmark G. B. Pant University of Agriculture & Technology, Pantnagar, India
Bhavdish N. Johri
Shubha P. Kale Xavier University of Louisiana, New Orleans, Louisiana, USA John C. Kennell Saint Louis University, St. Louis, Missouri, USA Viswanath P. Kurup Medical College of Wisconsin and VA Medical Center, Milwaukee, Wisconsin, USA B. Franz Lang
Canadian Institute for Advanced Research, Universite´ de Montre´al, Montre´al, Que´bec, Canada Universite´ du Littoral Coˆte d’Opale, Calais CEDEX, France
Fre´de´ric Laruelle
Jessica Leigh Canadian Institute for Advanced Research, Universite´ de Montre´al, Montre´al, Que´bec, Canada Carmen Limo´n VTT Biotechnology, Finland Dorothy M. Lo¨sel
University of Sheffield, Sheffield, United Kingdom
Benjamin C.K. Lu University of Guelph, Guelph, Ontario, Canada Robert L. Mach
Institute for Chemical Engineering, Vienna Technical University, Vienna, Austria
Bhawana Malhotra
University of Delhi South Campus, New Delhi, India
J. F. Martı´n University of Leo´n, and INBIOTEC, Leo´n, Spain Je´roˆme Muchembled Helena Nevalainen
Institut Charles Quentin, Pierrefonds, France Macquarie University, Sydney, Australia
T. B. Ng The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
© 2004 by Marcel Dekker, Inc.
University of Ulster, Coleraine, United Kingdom
Poonam Nigam
Mobidiag Limited, Biomedicum Helsinki, Helsinki, Finland
Simo Nikkari
Yoshimi Niwano Sato Pharmaceutical Co., Ltd., Tokyo, Japan Hiroyuki Ogawa NCIMB Japan Co., Ltd., Shizuoka, Japan A. G. Palma-Carlos I Clinica Me´dica Universita´ria e Centro de Hematologia e Imunologia, Faculdade de Medicina, Lisboa, Portugal M. Laura Palma-Carlos I Clinica Me´dica Universita´ria e Centro de Hematologia e Imunologia, Faculdade de Medicina, Lisboa, Portugal Gary A. Payne North Carolina State University, Raleigh, North Carolina, USA Merja Penttila¨ VTT Biotechnology, VTT, Finland Jure Piskur
BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark The Australian Wine Research Institute, Adelaide, Australia
Isak S. Pretorius
Seema Rawat G. B. Pant University of Agriculture & Technology, Pantnagar, India Malcolm Richardson University of Helsinki, Helsinki, Finland Tim Robinson University of Ulster, Coleraine, United Kingdom Naiara Rodriguez-Ezpeleta Que´bec, Canada
Canadian Institute for Advanced Research, Universite´ de Montre´al, Montre´al,
Jose´ Ruiz-Herrera Centro de Investigacio´n y de Estudios Avanzados del Instituto Polite´cnico Nacional, Irapuato, Gto., Mexico Roberto Ruiz-Medrano Centro de Investigacio´n y de Estudios Avanzados del Instituto Polite´cnico Nacional, Campus Me´xico, D. F., Mexico Michel Sancholle Universite´ du Littoral Coˆte d’Opale, Calais CEDEX, France Rajendra K. Saxena University of Delhi South Campus, New Delhi, India Christine Schimek
Institut fu¨r Mikrobiologie, Friedrich-Schiller-Universita¨t Jena, Jena, Germany
Esther Segal Tel Aviv University, Tel Aviv, Israel Elias Seif Canadian Institute for Advanced Research, Universite´ de Montre´al, Montre´al, Que´bec, Canada Dalel Singh
Haryana Agricultural University, Hisar, India
Gautam B. Singh David Smith
Oakland University, Rochester, Michigan, USA
CABI Bioscience UK Centre, Egham Surrey, United Kingdom
Junta Sugiyama Shizuoka, Japan Valentino Te’o
The University Museum, The University of Tokyo, Tokyo and NCIMB Japan Co., Ltd., Macquarie University, Sydney, Australia
Richard B. Todd
Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
Ne´stor V. Torres
Universidad de La Laguna, Tenerife, Canary Islands, Spain
Gustavo Viniegra-Gonza´lez Universidad Auto´noma Metropolitana, Iztapalapa, D.F., Me´xico
© 2004 by Marcel Dekker, Inc.
Eberhard O. Voit
Medical University of South Carolina, Charleston, South Carolina, U.S.A.
Johannes Wo¨stemeyer Hideyo Yamaguchi Oded Yarden
Institut fu¨r Mikrobiologie, Friedrich-Schiller-Universita¨t Jena, Jena, Germany
Institute of Medical Mycology, Teikyo University, Tokyo, Japan
The Hebrew University of Jerusalem, Rehovot, Israel
Susanne Zeilinger Institute for Chemical Engineering, Vienna Technical University,Wien, Austria Alexander Schulz
The Royal Veterinary and Agricultural University, Copenhagen, Denmark
© 2004 by Marcel Dekker, Inc.
1 Cell Biology of Hyphae Oded Yarden The Hebrew University of Jerusalem, Rehovot, Israel
1
INTRODUCTION
Members of the fungal kingdom are present in almost every conceivable niche. Even though fungi are remarkably diverse, many fungi share common cellular characteristics that are instrumental to the success of fungal growth, development, proliferation, and survival. The purpose of this introductory chapter is to provide the reader with an overview of some of the fundamental aspects of one of the predominant forms of fungal structures—hyphae. The introductory chapter discusses the attributes that are common to many fungi as well as other organisms while also emphasizing some of the features that are unique to fungal species, as compared to other eukaryotes (some of the details will be discussed in depth in the following chapters of this book). Perhaps the primary recognizable difference between the hyphal “cell” and cells of other organisms is the predominantly coenocytic nature of the former. Characteristically, the hyphal cell harbors multiple nuclei that are evenly or unevenly distributed over relatively long distances of cytoplasmic continuity. Nonetheless, in this chapter, the term “cell” is used while discussing some of the fundamental as well as more unique attributes of hyphae. Identifying and understanding the nature of these attributes, and in particular, the regulatory mechanisms involved in orchestrating the growth of the fungal filament is an important step in the process of our intervention in fungal biology, be it curbing detriments or enhancing benefits these organisms are capable of exhibiting.
2
THE CELL WALL
The cell wall is a characteristic structure present in many organisms whose life style to grow in an environment with continuously changing water potential can be
© 2004 by Marcel Dekker, Inc.
described as an absorptive one. Thus, the accumulation of large concentrations of osmotically active molecules requires the presence of a structure that will assist in maintaining the integrity of the cell membranes. In addition, the adventurous, and at times, invasive proliferation of the fungal filament in a variety of diverse environments requires the presence of effective mechanisms to defend the fungal cell from external perils. The cell wall is a prime example of an efficient mechanical exocellular defense system. Understanding the structure of the cell wall and the synthesis of its components is essential for elucidation of the processes involved in fungal growth and development. This understanding includes the fundamental aspects of filament elongation and branching as well as various aspects of differentiation, pathogenicity, absorption, and secretion.
2.1
Composition
The fungal cell wall accounts for approximately 25% of the mycelial dry weight. Approximately 80% of the cell wall dry weight is comprised of polysaccharides (Ruiz-Herrera 1992). The remaining 20% is comprised of proteins, lipids, and various inorganic salts. The predominant carbohydrate polymers found in different fungi are various forms of glucans and chitin. These sugars, synthesized and positioned in a nonuniform, yet highly regulated manner provide the external skeleton of the hyphal cell and are synthesized mainly at the apical region of the growing hyphae. Nonetheless, additional components (in particular—cell wall-associated proteins) are involved in determining the cell surface properties of the growing or nascent hypha. Cell wall associated proteins are involved in the restriction of cell permeability to detrimental compounds and/or proteins present in the environment. These cell wall proteins are also
involved in recognition of other fungi and regulation of processes such as anastomosis, sexual and asexual partner recognition, and interactions (e.g., recognition and adherence) with various hosts (Lora et al. 1995; Saupe et al. 1996). The interactions between fungal cell wall proteins and potential hosts is predominantly based on protein – protein recognition, even though there are convincing records of carbohydrate – protein interactions with the carbohydrate supplied by either the fungus or the host (Cormack et al. 1999).
2.2
Synthesis
As the extension of the hyphal filament occurs mainly in the apical region, most of the biosynthetic machinery (and most likely some degradative machinery as well) involved in this process is trafficked to that region of the apical cell. As the main components of the hyphal cell are glucan and chitin, the glucan and chitin synthases must be positioned properly (in the vicinity of the extension or repair areas) and their activity regulated so as to produce the relevant polymer in a sitespecific manner. The mechanism by which the polymers are extruded is yet unclear. The presence of several chitin synthases in filamentous fungi has been documented at the respective genomic databases (NCBI and other, specific, databases as mentioned in Section 7.3 of this chapter). Based on the available information, Neurospora crassa and Aspergillus fumigatus each have seven genes encoding for chitin synthases, whereas Saccharomyces cerevisiae has three. The differential expression and functional consequence of chitin synthase gene inactivation have demonstrated that different chitin synthases have different roles during fungal growth and development (for a detailed perspective see Chapter 30). Some chitin synthases are essential for maintaining proper hyphal rigidity and form and are required for hyphal elongation. The specific roles of other members of this gene family have yet to be elucidated. The cell wall biosynthetic (chitin and glucan synthases) as well as cell wall lytic (chitinases and glucanases) enzymes required for cell elongation and branching processes are conveyed to the required location, and at least in some cases, compartmentalized trafficking is carried out in membranous vesicles (Sietsma et al. 1996). The wall at the tip is plastic allowing the extension of the cell by insertion of new material. As extension progresses, the material at the former position of the apex is progressively rigidified as it becomes the lateral wall of the growing cell. This rigidification is brought about by the covalent cross-linking of wall materials, especially chitin and b(1 – . 3) glucans, and the hydrogen bonding of adjacent polysaccharide chains, especially chitin, to give microfibrils. Many of the cell wall-associated proteins are heavily glycosylated. Many of the proteins secreted to the external face of the plasma membrane are linked via a remnant of the glycosylphosphatidylinositol anchor to the polysaccharide cell wall component. N-Glycosylation of proteins in the fungal endoplasmic reticulum is most likely very similar to that observed in mammalian cells, yet the process occurring © 2004 by Marcel Dekker, Inc.
in the Golgi apparatus is different than that described in mammals (Dean 1999). O-Glycosylation also occurs in filamentous fungi and is mediated by a conserved family of protein-mannosyl-transferases (Strahl-Bolsinger et al. 1999).
2.3
Hydrophobins
Hydrophobins are among the unique protein components of the fungal cell wall. These small proteins, secreted during a variety of developmental processes are present in most filamentous fungi and have, so far, not been found in nonfungal species (Talbot 1999). These proteins play essential roles in fungal adherence, development of aerial structures, and infection of host plants by phytopathogens (Ebbole 1997). Fungal hydrophobins are hydrophobic in nature and can be defined by the presence of eight cysteine residues that are spaced in a particular manner within the amino acid sequence. They have been divided into two classes, based on solubility characteristics brought about by differences in cysteine residue spacing and distribution of hydrophobic and hydrophilic amino acids within the hydrophobin polypeptide sequences (Wo¨sten et al. 1999). Beyond the involvement of fungal hydrophobins in natural processes of fungal growth and proliferation, the unique attributes of these proteins have been the basis of several suggested industrial applications. These include the use of hydrophobins as molecular anchor points for industrial proteins/enzymes, by attaching them to hydrophobic plastic surfaces. Other potential uses include the production of a natural protein coating over artificial organs or other transplants (Kershaw and Talbot 1998). Though many structural components and organizational features are common to a wide range of fungi, differences in cell walls can be observed among different fungal species. Furthermore, the composition and structure of the cell wall can diverge immensely during the growth and development of the fungal colony.
3
THE PLASMA MEMBRANE
The presence of a cell wall provides the fungal cell with the ability to survive and grow without the need to equalize the cellular osmotic potential to that of its environment. In fact, the difference in osmotic potential contributes to the ability of the hyphal cell to elongate and branch by creating turgor pressure. The primary active barrier between the fungal cell and the environment is the plasma membrane. As seen in other organisms, the plasma membrane is a selective divide involved in flow of material and information between the cell and its environment. The maintenance of a plasma membrane potential and appropriate ion gradients are the basis of the ability to transport solutes in and out of the fungal cell. This ability is achieved via a variety of proton pumps, carrier proteins, and ion channels. N. crassa has been a prime model for analysis of
proton pumping and membrane potential (Davis 2000). The maintenance of a pH gradient and a high membrane potential (