Advances in fungal biotechnology for industry, agriculture, and medicine (New York, 2004). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаAdvances in fungal biotechnology for industry, agriculture, and medicine / ed. by J.S.Tkacz, L.Lange. - New York: Kluwer/Plenum, 2004. - xxii, 445 p.: ill. - Incl. bibl. ref. - Ind.: p.425-445. - Пер. загл.: Достижения в области грибных биотехнологий для промышленности, сельского хозяйства и медицины. - ISBN 0-306-47866-8
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
Preface ....................................................... xix

Part I. Genetic Technology
1. Practical Molecular Taxonomy of Fungi
   David M. Geiser
   1  Introduction .............................................. 3
   2  Identifying a Fungus to Species—What does it Mean? ........ 3
      2.1  Useful Species Definitions ........................... 3
      2.2  Genealogical Concordance as a Means to Recognize
           Fungal Species ....................................... 4
      2.3  Molecular Taxonomy in Practice ....................... 6
   3  How do I Identify an Unknown Fungus? ...................... 6
      3.1  The Molecular Toolbox ................................ 7
           3.1.1  DNA Sequence Tools ............................ 7
           3.1.2  Genotyping Methods: Comparing and Identifying
                  Isolates within a Species ..................... 9
      3.2  Using the Toolbox ................................... 11
           3.2.1  Tools for Identifying any Fungus ............. 11
           3.2.2  Tools for Identifying Fungi in a Particular
                  Taxonomic Group of Intensive Study ........... 12
   4  What is Next? ............................................ 12
   References .................................................. 13

2. Genomics of Filamentous Fungi
   Ulrich Schulte
   1  Introduction ............................................. 15
   2  Genomic Projects Focusing on Fungi ....................... 16
   3  Genome Structure ......................................... 18
   4  Gene Identification and Annotation ....................... 19
   5  Gene Complement of a Filamentous Fungus .................. 21
   6  Novel Aspects of Fungal Biology .......................... 26
   7  Summary .................................................. 27
   References .................................................. 27

3. A Molecular Tool Kit for Fungal Biotechnology
   John E. Hamer
   1  Introduction ............................................. 31
   2  Vectors and Transformation ............................... 32

   1  Gene Cloning Tools for Genomic Approaches ................ 32
   4  Fungal Transposons as Tools .............................. 33
   5  Tools for Identifying Essential Genes .................... 34
      5.1  Generating Conditional Lethal Mutants ............... 34
      5.2  Inference ........................................... 34
      5.3  Using Controllable Promoters ........................ 34
      5.4  Post-Transcriptional Gene Silencing (PTGS) .......... 35
   6  Genome-Based Tools ....................................... 35
      6.1  Genome-Wide Insertional Mutagenesis ................. 36
      6.2  Genome-Shuffling .................................... 36
   7  Summary .................................................. 37
   References .................................................. 37

4. Transformation Mediated by Agrobacterlum tumefaclens
   Paul J.J. Hooykaas
   1  Introduction ............................................. 41
   2  Agrobacterium ............................................ 42
   3  Host Range ............................................... 44
   4  T-DNA Transfer Resembles Bacterial Conjugation ........... 44
   5  Accessory Functions Enabling Trans-Kingdom DNA Transfer .. 49
   6  Protein Translocation from Agrobacterium into Host Cells . 50
   7  T-DNA Integration ........................................ 51
   8  Agrobacterium-Bastd Vector Systems ....................... 52
   9  Transformation of Yeasts and Filamentous Fungi ........... 54
   10 Concluding Remarks ....................................... 57
   References .................................................. 58

Part II. Special (Secondary) Metabolism

5. Fungal Polyketide Synthases in the Information Age
   Russell J. Cox and Frank Glod
   1  Introduction ............................................. 69
      1.1  Secondary Metabolites ............................... 69
      1.2  Polyketides ......................................... 71
      1.3  Types of Polyketide Synthase ........................ 72
   2  Non-Fungal PKS ........................................... 73
   3  Fungal PKS ............................................... 75
      3.1  6-Methylsalicyclic Acid Synthase .................... 76
      3.2  Fungal PKS Involved in Biosynthesis of Conidial
           Pigment and Melanin ................................. 77
      3.3  Fungal Polyketide Mycotoxins—Norsolorinic Acid
           Synthase (NAS) ...................................... 78
      3.4  Polyketide Synthase in T-Toxin Production ........... 79
      3.5  Polyketide Synthase in Fumonisin Production ......... 79
      3.6  Lovastatin Synthases ................................ 80
   4  Novel Methods for Accessing PKS Genes .................... 81
      4.1  Problems Associated with Cloning Fungal PKS Genes ... 81
      4.2  Early Efforts to Develop Fungal PKS Probes .......... 82
      4.3  Assessing Biosynthetic Potential .................... 85
           4.3.1  Prokaryotes .................................. 85
           4.3.2  Lichens ...................................... 85
           4.3.3  Insect and Nematode Associated Fungi ......... 86
           4.3.4  Endophytic Fungi ............................. 88
      4.4  Biosynthetically Informed Approaches for Accessing
           Fungal PKS Genes .................................... 88
           4.4.1  KS-Specific Primers .......................... 88
           4.4.2  KR-Specific Primers .......................... 90
           4.4.3  CmeT-Specific Primers ........................ 90
           4.4.4  Lessons and Outlook .......................... 92
5  The Genomic Era ............................................. 92
   References .................................................. 93

6  More Functions for Multifunctional Polyketide Synthases
   Isao Fujii, Akira Watanabe, and Yutaka Ebizuka
   1  Introduction ............................................. 97
   2  Architecture and Functions of Fungal Polyketide
      Synthases ............................................... 100
      2.1  MS AS/OAS Polyketide Synthases ..................... 100
      2.2  Polyketide Synthases for Aromatic Multi-Ring
           Products (AR-PKSs) ................................. 100
           2.2.1  Pentaketide 1,3,6,8-Tetrahydroxynaphthalene
                  Synthases ................................... 101
           2.2.2  Heptaketide Naphthopyrone Synthases ......... 102
           2.2.3  PKSs Involved in Aflatoxin Biosynthesis ..... 103
      2.3  Polyketide Synthases for Reduced Products
           (RD-PKSs) .......................................... 103
           2.3.1  T-toxin PKS ................................. 104
           2.3.2  PKSs Involved in Lovastatin Biosynthesis .... 105
           2.3.3  Fumonisin PKS ............................... 105
           2.3.4  RD-PKS from Altemaria solani ................ 106
   3  More Functions for Fungal Polyketide Synthases .......... 106
      3.1  Claisen Cyclase Domain in AR-PKSs .................. 107
      3.2  More Functions for AR-PKSs ......................... 110
           3.2.1  Starter Units ............................... 110
           3.2.2  N-Termini ................................... 111
           3.2.3  InterdomainRegions .......................... 111
           3.2.4  ACPDomains .................................. 111
      3.3  C-Methyltransferase Domains in RD-PKSs ............. 113
      3.4  PSED (Peptide Synthetase Elongation Domain)-Like
           Domains in RD-PKSs ................................. 114
      3.5  "Diels-Alderase" in RD-PKSs ........................ 115
   4  Concluding Remarks ...................................... 118
   Acknowledgments ............................................ 120
   References ................................................. 120

7  Peptide Synthesis Without Ribosomes
   Jonathan D. Walton, Daniel G. Panaccione, and Heather
   E. Hallen
   1  Introduction ............................................ 127
   2  Overview of Non-Ribosomal Peptide Synthetases ........... 129
   3  The "Non-Ribosomal Code" for Fungal NRP Synthetases ..... 132
   4  Parsing Fungal NRP Synthetases .......................... 136
      4.1  Guideline 1 ........................................ 136
      4.2  Guideline 2 ........................................ 137
      4.3  Guideline 3 ........................................ 137
   5  Strategies to Identify NRP Synthetases and Genes ........ 138
   6  Tailoring Enzymes and Auxiliary Domains ................. 139
      6.1  N-Methylation ...................................... 139
      6.2  Epimerization ...................................... 140
      6.3  Other Tailoring Reactions of Fungal NRP
           Synthetases ........................................ 140
      6.4  Pantetheinylation .................................. 141
   7  Regulation .............................................. 142
   8  Status of Research on Selected Fungal Systems ........... 143
      8.1  AM-Toxin ........................................... 143
      8.2  Cyclosporin ........................................ 144
      8.3  Destruxins ......................................... 145
      8.4  Enniatins .......................................... 145
      8.5  Ergopeptines ....................................... 146
      8.6  НС-Toxin ........................................... 148
      8.7  Penicillin and Cephalosporin ....................... 149
      8.8  Peptaibols ......................................... 150
   9  Evolution of NRPs and NRP Synthetases ................... 151
      9.1  Clustering ......................................... 151
      9.2  Evolution of Secondary Metabolite Pathways ......... 152
   10 NRP Synthetases in the Genomics Age ..................... 154
   Acknowledgments ............................................ 154
   References ................................................. 155

8. Isoprenoids: Gene Clusters and Chemical Puzzles
   D. Barry Scott, Geoffrey B. Jameson, and Emily J. Parker
   1  Introduction ............................................ 163
   2  Sesquiterpenes .......................................... 165
      2.1  Trichothecenes ..................................... 165
           2.1.1  Chemical Diversity .......................... 165
           2.1.2  Gene Clusters ............................... 166
           2.1.3  Biosynthesis of T2-Toxin .................... 167
           2.1.4  Regulation .................................. 172
      2.2  Aristolochenes ..................................... 173
   3  Diterpenes .............................................. 174
      3.1  GibbereUins ........................................ 174
           3.1.1  Chemical Diversity .......................... 174
           3.1.2  Gene Cluster ................................ 175
           3.1.3  Biosynthesis of GA3 ......................... 175
           3.1.4  Regulation .................................. 179
      3.2  Indole-Diterpenes .................................. 179
           3.2.1  Chemical Diversity .......................... 180
           3.2.2  Gene Cluster ................................ 180
   4. Tetraterpenes ........................................... 184
      4.1  Carotenoids ........................................ 184
           4.1.1  Chemical Diversity .......................... 185
           4.1.2  Biosynthetic Pathway ........................ 185
   5  Proteins of Isoprenoid Biosynthetic Pathways ............ 189
      5.1  Initiation of Prenyl Transfer ...................... 189
      5.2  Prenyl Transferase Structure and Classification .... 190
      5.3  Trichodiene Synthase ............................... 191
      5.4  Aristolochene Synthase ............................. 192
   6  Final Remarks ........................................... 192
      Acknowledgments ......................................... 193
      References .............................................. 193

Part III. Enzymes and Green Chemistry

9  Heterologous Expression and Protein Secretion in
   Filamentous Fungi
   Wendy Thompson Yoder and Jan Lehmbeck
   1  Introduction ............................................ 201
   2  The Past Decade ......................................... 202
   3  Development of a New Fungal Expression Host: Fusarium
      venenatum Nirenberg ..................................... 208
      3.1  Selection Criteria ................................. 208
      3.2  Heterologous Expression ............................ 209
      3.3  Improved Morphological Mutants ..................... 209
      3.4  Selectable Markers ................................. 209
      3.5  Targeted Gene Deletions ............................ 210
      3.6  GRAS Status for the First Heterologous Enzyme
           Produced in F. venenatum ........................... 210
      3.7  The First Commercial Recombinant F. venenatum
           Product ............................................ 210
      3.8  Fusarium venenatum Genomics ........................ 210
   4  "To Infinity and Beyond" ................................ 211
   5  Conclusions ............................................. 212
   References ................................................. 213

10 Artificial Evolution of Fungal Proteins
   Jesper Vind
   1  Introduction ............................................ 221
   2  Artificial Evolution in General ......................... 221
      2.1  Idea Generation .................................... 221
      2.2  In Vitro Generation of Gene Variants ............... 222
   3  In Vitro Mutagenesis and Expression of Fungal Proteins .. 222
      3.1  Characterization of Protein Variants Expressed in
           Yeast .............................................. 222
      3.2  Characterization of Protein Variants Expressed
           in Filamentous Fungi ............................... 224
      3.3  Library Generation in Filamentous Fungi ............ 225
   4  In Vivo Mutagenesis in Fungi ............................ 226
      4.1  In Vivo Shuffling in Yeast ......................... 226
      4.2  In Vivo Shuffling in Neurospora .................... 226
      4.3  In Vivo Mutagenesis with the RIP System ............ 228
      4.4  In Vivo Mutagenesis with the Mismatch Repair
           System ............................................. 228
   5  Future in Artificial Evolution of Fungal Proteins ....... 231
   References ................................................. 232

11.Biocatalysis and Biotransformation
   Frieder Schauer and Rainer Borriss
   1  Preface ................................................. 237
   2  Fungal Enzymes and Biotransformations—An Introduction ... 237
   3  Glycosyl Hydrolases ..................................... 242
      3.1  Starch Hydrolysis: Amylases and Glucoamylases ...... 244
      3.2  Cellulose and Cellulases ........................... 245
           3.2.1  Cellulases in Textile and Laundry
                  Biotechnology ............................... 246
      3.3  Hydrolysis of Hemicellulose: Xylanases and
           Mixed-Linked β-Glucanases .......................... 246
           3.3.1  Xylanases ................................... 246
           3.3.2  Application: Delignification of Kraft
                  Pulps by Trichoderma Xylanases .............. 247
           3.3.3  Mixed Linked β-Glucan Hydrolyzing Enzymes ... 247
           3.3.4  Application of Cellulases and
                  Hemicellulases in Animal Feed
                  Biotechnology ............................... 249
      3.4  Cell Wall Lytic Enzymes ............................ 249
           3.4.1  Macerating Enzymes in Fruit and Vegetable
                  Processing .................................. 249
   4  Phosphorous Mobilization: Phytases ...................... 249
      4.1  Engineering of Improved Functionality in
           Aspergillus Phytase ................................ 252
   5  Lipases (Triacylglycerol Hydrolases, EC 3.1.1.3) ........ 253
   6  Proteases ............................................... 254
   7  Degradation of Lignocellulose: Ligninolytic Enzymes ..... 255
      7.1  Lignin Peroxidase and Manganese Peroxidase ......... 256
      7.2  Laccase ............................................ 256
           7.2.1  Distribution ................................ 257
           7.2.2  Biological Function of Laccase .............. 257
           7.2.3  Isoenzymes .................................. 258
           7.2.4  Characterization and Some Biochemical
                  Properties .................................. 258
           7.2.5  Regulation of Laccase Production ............ 259
           7.2.6  Laccase Mediator Systems .................... 259
           7.2.7  Delignification of Ligninocellulosics by
                  Laccase ..................................... 260
           7.2.8  Purification of Colored Waste Waters ........ 260
           7.2.9  Textile Dye Decolorization .................. 260
           7.2.10 Transformation and Inactivation of Toxic
                  Environmental Pollutants .................... 260
           7.2.11 Beverage and Food Treatment ................. 261
           7.2.12 Laccase-Based Biosensors .................... 261
           7.2.13 Synthesis of New Chemicals by Laccase ....... 261
           7.2.14 Desulfurization and Solubilization of Coal .. 262
   8  Utilization of Aromatic and Aliphatic Compounds and
      Hydrocarbons ............................................ 262
   9  Inactivation of Fungal Biocontrol Agents ................ 263
      9.1  Creosote ........................................... 263
      9.2  Pentachlorophenol .................................. 264
      9.3  Inorganic Wood Preservatives ....................... 264
      9.4  Disinfectants and Deodorants ....................... 265
      9.5  Fungicides in Agriculture and Medicine ............. 265
      9.6. Food Preservatives ................................. 265
   10 Biotransformation of Biphenyls by Fungi ................. 266
      10.1 Biphenyl ........................................... 266
      10.2 Polychlorinated Biphenyls .......................... 268
   11 Oxidation of Dibenzofurans and Dibenzodioxins ........... 269
   12 Biotransformation of Diphenyl Ethers and Phenoxy
      Herbicides .............................................. 272
   13 Dehalogenation of Aromatic Xenobiotics .................. 275
   14 Trends and Future Developments .......................... 276
      14.1 Novel Fungal Enzymes: Screening, Development, and
           Specific Features .................................. 277
      14.2 Screening of Fungi Producing Improved Phytases ..... 278
      14.3 Diversity of Microbial Enzymes Catalyzing
           Stereoselective Reactions .......................... 279
      14.4 Lactonase in D-Pantothenic Acid Production ......... 279
      14.5 Aldehyde Reductase in the Production of Chiral
           Alcohols ........................................... 279
      14.6 Laccase-Catalyzed Heteromolecular Coupling of
           Molecules .......................................... 279
      14.7 Heterologous Expression of Fungal Ligninolytic
           Enzymes ............................................ 280
      14.8 Impact of DNA Recombinant Techniques ............... 280
      14.9 Expression of Aspergillus Phytase in Transgenic
           Plants ............................................. 281
      14.10 Gene Libraries .................................... 282
      14.11 Biomolecular Engineering .......................... 282
      14.12 Concept of Directed Evolution ..................... 283
   References ................................................. 283

12 Organic Acid Production by Filamentous Fungi
   Jon K. Magnuson and Linda L. Lasure
   1  Introduction ............................................ 307
   2  Commercial Successes: Organic Acids from Filamentous
      Fungi ................................................... 308
      2.1  Citric Acid ........................................ 309
      2.2  Gluconic Acid ...................................... 310
      2.3  Itaconic Acid ...................................... 310
      2.4  L-Lactic Acid ...................................... 311
      2.5  Market Prospects ................................... 311
   3  Biochemistry and Genetics of Organic Acid Production
      by Filamentous Fungi .................................... 312
      3.1  Aspergillus and Organic Acid Production ............ 312
           3.1.1  Citric Acid ................................. 312
           3.1.2  Oxalic Acid ................................. 319
           3.1.3  Gluconic Acid ............................... 322
           3.1.4  Itaconic Acid ............................... 323
      3.2  Rhizopus and Organic Acid Production ............... 325
           3.2.1  L-Lactic Acid ............................... 325
           3.2.2  Fumaric Acid ................................ 328
           3.2.3  L-Malic Acid ................................ 329
           3.2.4  Succinic Acid ............................... 330
           3.2.5  (—)-trans-2,3-Epoxysuccinic Acid and
                  meso-Tartaric Acid .......................... 330
   4  Final Perspective ....................................... 332
   References ................................................. 333

13 Flavors and Fragrances
   Ralf G. Berger and Holger Zorn
   1  Introduction ............................................ 341
   2  Biotransformation of Terpenoids by Fungi ................ 343
   3  Biosynthesis of Terpenyl Esters ......................... 348
   4  Generation of Aromatic Flavor Compounds ................. 349
   5  Flavor Compounds from Other Chemical Classes ............ 353
   6  Bioprocess Technology ................................... 353
   7  Conclusion .............................................. 355
   References ................................................. 355

Part IV. Host-Fungal Interactions
14 Human Mycoses: The Role of Molecular Biology
   Donald C. Sheppard, Ashraf S. Ibrahim, and John
   E. Edwards Jr.
   1  Introduction ............................................ 361
   2  Goals in the Study of Pathogenic Filamentous Fungi ...... 362
      2.1  Identification of Virulence Factors ................ 362
      2.2  Identification of Other Drug Targets ............... 362
   3  The Genus Aspergillus ................................... 362
      3.1  Aspergillosis: Spectrum of Disease ................. 363
      3.2  Aspergilloma ....................................... 363
      3.3  Invasive Aspergillosis (IA) ........................ 363
           3.3.1  Epidemiology and Significance ............... 363
           3.3.2  Pathophysiology ............................. 363
           3.3.3  Virulence Factors of A. fumigatus ........... 364
           3.3.4  Clinical Presentation of IA ................. 364
           3.3.5  Therapy of IA ............................... 364
      3.4  Molecular Techniques for the Study of Aspergillus
           sp ................................................. 366
           3.4.1  Selection Markers for A. fumigatus .......... 366
           3.4.2  Transformation Techniques ................... 369
           3.4.3  Parasexual Genetics ......................... 370
           3.4.4  Signature-Tagged Mutagenesis ................ 371
           3.4.5  Reporter Gene Systems ....................... 372
           3.4.6  Transposable Elements in Aspergilli ......... 373
           3.4.7  Complementation and Heterologous
                  Expression in Aspergilli .................... 373
           3.4.8  Genome Sequencing ........................... 374
   4  The Agents of Mucormycosis .............................. 375
      4.1  Molecular Techniques for the Study of
           Mucormycosis ....................................... 376
           4.1.1  Transformation Techniques ................... 377
           4.1.2  Sexual Cycle ................................ 378
           4.1.3  Heterologous Expression ..................... 378
           4.1.4  Summary ..................................... 379
   5  Other Pathogenic Filamentous Fungi ...................... 379
   6  Future Directions ....................................... 379
   References ................................................. 379

15 Molecular Interactions of Phytopathogens and Hosts
   Joanna M. Jenkinson and Nicholas J. Talbot
   1  Introduction ............................................ 385
      1.1  The Life Cycles of Magnaporthe grisea and
           Ustilago maydis .................................... 386
   2  Pathogenicity Factors ................................... 387
      2.1  Regulators of Infection ............................ 387
           2.1.1  The cAMP Response Pathway ................... 387
           2.1.2  PMK1 and MAP Kinase Pathways in Fungal
                  Pathogens ................................... 389
           2.1.3  РАШ-Related MAP Kinases in Other
                  Phytopathogenic Fungi ....................... 392
           2.1.4  Alternative МАРК Pathways in M. grisea ...... 392
           2.1.5  Nutritional Regulatory Genes ................ 393
      2.2  Pathogen-Specific Molecules ........................ 394
           2.2.1  Toxins and Host-Specific Toxins ............. 394
      2.3  Plant Recognition Evasion .......................... 395
           2.3.1  Saponin Detoxification ...................... 395
           2.3.2  Phytoalexin Detoxification .................. 395
      2.4  Proteins of Unknown Function ....................... 396
      2.5  Pathogen Associated Molecular Patterns ............. 397
           2.5.1  Plant Resistance Mechanisms ................. 397
           2.5.2  R Gene and Avr Gene Signaling ............... 398
   3  Genomics of Phytopathogens .............................. 399
   4  Future Prospects ........................................ 400
   References ................................................. 400

16 Structural and Functional Genomics of Symbiotic Arbuscular
   Mycorrhizal Fungi
   V. Gianinazzi-Pearson, C. Azcon-Aguilar, G. Becard,
   P. Bonfante, N. Ferrol, P. Franken, A. Gollotte,
   L.A. Harrier, L. Lanfranco, and D. van Tuinen
   1  Introduction ............................................ 405
   2  Genome Structure and Organization ....................... 407
   3  Fungal Genes in the Symbiotic Context ................... 408
      3.1  Targeted Analyses of Gene Expression ............... 408
      3.2  Transcriptome Profiling ............................ 412
   4  Manipulating the Symbiotic Genome ....................... 414
   5  Endobacterial Genes ..................................... 417
   6  Conclusions ............................................. 418
      Acknowledgments ......................................... 419
      References .............................................. 419

Index ......................................................... 425


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