Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine

Edited by

JAN S. TKACZ Department of Biologics Research Merck Research Laboratories Rahway, New Jersey and

LENE LANGE Department of Molecular Biotechnology Novozymes AlS Bagsvaerd, Denmark

Springer Science+Business Media, LLC Library of Congress Cataloging-in-Publication Data

Advances in funga! biotechnology for industry, agriculture, and medicine / edited by Jan S. Tkacz and Lene Lange. p. cm. lncludes bibliographical references and index. ISBN 978-1-4613-4694-4 ISBN 978-1-4419-8859-1 (eBook) DOI 10.1007/978-1-4419-8859-1 1. Fungi-Biotechnology. 1. Tkacz, Jan S. II. Lange, Lene.

TP248.27.F86A362oo4 660.6'2--<1c22 2003060293

ISBN 978-1-4613-4694-4 ©2004 Springer Science+Business Media New York Origina11y published by Kluwer Academic / Plenum Publishers, New York in 2004 Softcover reprint of the hardcover 1st edition 2004 http://www.wkap.nl/ ill 9 8 7 6 5 4 3 2 1

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Concepcion Azcon-Aguilar The University of Tokyo CSIC,Departamento de Microbiologia del 7-3-1 Hongo, Bunkyo-ku Suelo y SistemasSimbioticos Tokyo 113-0033 EstacionExperimental del Zaidin Japan ProfesorAlbareda I 18008Granada John E. Edwards, Jr. Spain Divisionof Infectious Diseases UCLASchool of Medicine Guillaume Becard Harbor-UCLA MedicalCenter Universite PaulSabatierlUMR 5546CNRS 1000WCarson St. Equipede MycologieVegetale Torrance CA 90502 Pole de Biotechnologie Vegetale 24 Cheminde Borde-Rouge Nuria Ferrol BP 17Auzeville CSIC, Departamento de Microbiologia del 31326 Castanet-Tolosan Sueloy SistemasSimbioticos France Estacion Experimental del Zaidin ProfesorAlbareda I Ralf G. Berger 18008Granada ZentrumAngewandte Chemie Spain Universitat Hannover Institut fur Lebensmittelchemie Philipp Franken Wunstorfer Strasse 14 Institute for Vegetable and Ornamental D-30453 Hannover Plants Germany Theodor-Echtermeyer-Weg I D-14979Grossbeeren Paola Bonfante Germany Universita degliStudidi Torino Dipartimento di BiologiaVegetale Isao Fujii Mycology IPP/CNR and Molecular GraduateSchool of Pharmaceutical Biology Sciences Viale Mattioli 25 The University of Tokyo 10125 Torino 7-3-1 Hongo, Bunkyo-ku Italy Tokyo 113-0033 Japan Rainer Borriss Instituteof Biology David M. Geiser Humboldt-University Berlin Departmentof Plant Pathology Chausseestrasse117 The Pennsylvania State University D-10055 Berlin 121 BuckhoutLaboratory Germany UniversityPark PA 16802 Russell J. Cox Vivienne Gianinazzi-Pearson School of Chemistry UMR 1088INRAlUniversite de University of Bristol BourgogneBBCE-IPM Cantock's Close, Clifton INRA-CMSE, BP 86510 Bristol 21065 Dijon cedex BS8 ITS France United Kingdom Frank Glod Yutaka Ebizuka School of Chemistry GraduateSchool of Pharmaceutical University of Bristol Sciences Cantock's Close, Clifton

v vi Contributors

Bristol,BS8 ITS Luisa Lanfranco United Kingdom Universita degliStudidi Torino Dipartimento di Biologia Vegetale Armelle Gollotte Mycology CSMT/CNR andMolecular UMR 1088INRAlUniversite de Bourgogne Biology BBCE-IPM VialeMattioli 25 INRA-CMSE, BP 86510 10125 Torino 21065Dijon cedex Italy France Linda L. Lasure Heather E. Hallen PacificNorthwest National Laboratory Department of EnergyPlant Research 902 BattelleBlvd. Laboratory P.O. Box 999, MSIN: K2-12 Michigan State University RichlandWA 99352 East LansingMI 48824 Jan Lehmbeck John E. Hamer Novozymes AlS, Krogshoejvej 36 Paradigm Genetics Inc. DK-2880, Bagsvaerd P.O. Box 14528 Denmark Research TrianglePark NC 27709 Jon K. Magnuson Lucy Alexandra Harrier PacificNorthwest National Laboratory The ScottishAgricultural College 902 BattelleBlvd. Biotechnology Department P.O. Box 999, MSIN: K2-12 Plant ScienceDivision Richland WA 99352 WestMains Road EH9 3JG Edinburgh Daniel G. Panaccione United Kingdom Division of Plant & Soil Sciences WestVirginia University 401 BrooksHall Paul J.J. Hooykaas P.O. Box 6058 Instituteof MolecularPlant Sciences Morgantown WV 26506-6058 ClusiusLaboratory Leiden University Emily J. Parker Wassenaarseweg 64 Instituteof Fundamental Sciences 2333AL Leiden Collegeof Sciences The Netherlands Massey University Private Bag II 222 Ashraf S. Ibrahim Palmerston North Division of Infectious Diseases NewZealand UCLASchool of Medicine 1000WCarson St. Frieder Schauer Torrance CA 90502 Instituteof Microbiology E.-M.-Amdt-University Greifswald Geoffrey B. Jameson E-L.-Jahn-Strasse 15 Instituteof Fundamental Sciences D-17487Greifswald Collegeof Sciences Germany MasseyUniversity PrivateBag II 222 Ulrich Schulte Palmerston North Institutfur Biochetnie NewZealand Heinrich-Heine-Universitlit D-40225 Dusseldorf Joanna M. Jenkinson Germany Schoolof Biological Sciences University of Exeter D. Barry Scott Washington SingerLaboratories Instituteof MolecularBioSciences Perry Road Collegeof Sciences, Exeter, EX4 4QG MasseyUniversity United Kingdom Private Bag II 222 Contributors vii

Palmerston North DK-2880 Bagsvaerd NewZealand Denmark Donald C. Sheppard Jonathan D.Walton Division of Infectious Diseases Department of Energy PlantResearch Harbor-UCLA Research and Education Laboratory Institute Michigan State University 1000W CarsonSt. East LansingMI 48824 Torrance CA 90502 Akira Watanabe Nicholas J.Talbot Structural Biology Laboratory Schoolof Biological Sciences The Salk Institutefor Biological University of Exeter Studies Washington SingerLaboratories San DiegoCA 92186-5800 Perry Road Exeter, EX4 4QG Wendy Thompson Yoder UnitedKingdom Novozymes BiotechInc. 1445DrewAve. Diederik van Tuinen DavisCA 95616 UMR 1088INRNUniversitede Bourgogne BBCE-IPM Holger Zorn INRA-CMSE, BP 86510 ZentrumAngewandte Chemie 21065Dijoncedex Universitat Hannover France Institutfur Lebensmittelchemie Wunstorfer Strasse14 JesperVind D-30453 Hannover Novozymes Germany NOVO Aile 1, lU.1.20 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 II 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

ix x Contents

3. 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-Based 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 RussellJ. Cox and FrankGlod 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 Contents xi

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. MSAS/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 Alternaria 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. Interdomain Regions 111 3.2.4. ACP Domains 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 HeatherE. Hallen 1. Introduction 127 2. Overview of Non-Ribosomal Peptide Synthetases 129 3. The "Non-Ribosomal Code" for Fungal NRP Synthetases 132 xii Contents

4. Parsing Fungal NRP Synthetases 136 4.1. Guideline I ...... 136 4.2. Guideline2...... 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. HC-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 I. 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 ofT2-Toxin ...... 167 2.1.4. Regulation 172 2.2. Aristolochenes 173 3. Diterpenes 174 3.1. Gibberellins 174 3.1.1. Chemical Diversity...... 174 3.1.2. Gene Cluster 175

3.1.3. Biosynthesis ofGA3 •.•• •• ••••••••• •• •• •. .•• .• •• •• •• ...... 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 Contents xiii

5. Proteins ofIsoprenoid 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. ThePastDecade...... 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 xiv Contents

11. Biocatalysis and Biotransformation FriederSchauerand RainerBorriss 1. Preface ...... 237 2. Fungal Enzymes and Biotransfonnations-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 I3-Glucanases 246 3.3.1. Xylanases ...... 246 3.3.2. Application: Delignification of Kraft Pulps by Trichoderma Xylanases ...... 247 3.3.3. Mixed Linked I3-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 Contents xv

9.6. Food Preservatives 265 10. Biotransformation of Biphenyls by Fungi ...... 266 10.1. Biphenyl ...... 266 10.2. Polychlorinated Biphenyls ...... 268 II. 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-PantothenicAcid 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 I. 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-LacticAcid 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. t -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 xvi Contents

13. Flavors and Fragrances Ralf G. Bergerand HolgerZorn 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, AshrafS. 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. Aspergilloina 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 Contents xvii

15. Molecular Interactions of Phytopathogens and Hosts Joanna M. Jenkinson and NicholasJ. Talbot 1. Introduction 385 1.1. The Life Cycles of Magnaporthe grisea and Ustilago maydis ...... 386 2. Pathogenicity Factors ...... 387 2.1. Regulators ofInfection ...... 387 2.1.1. The cAMP Response Pathway 387 2.1.2. PMKI and MAP Kinase Pathways in Fungal Pathogens ...... 389 2.1.3. PMKI-RelatedMAP Kinases in Other Phytopathogenic Fungi...... 392 2.1.4. Alternative MAPK 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. Azeon-Aguilar, G. Becsrd, P. Bonfante, N. Ferrol, P. Franken, A. Go/lotte, L.A. Harrier, L. Lanfraneo, 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 Preface

Over the past 15 years, the tools of molecular biology have been successfully adapted for the study of filamentous fungi. Their application has elevated the status of fungal genetics from a fascinating and, at times, truly insightful field of study, but one focused upon only a handful of model organisms, to a discipline spanning the broad spectrum of organisms and topics that engage the interest of mycologists as a whole and biotechnologists in general. Molecular genetics has provided a toolbox of immensely powerful experimental approaches and, additionally, has become a magnet attracting young investigators to for­ merly intractable or unstudied organisms. It has embraced virtually all groups of economically, medically, and environmentally important fungi and is having a significant impact on commercial bioprocesses. Fungi, by virtue of their metabolic versatility, ecological diversity, complex life cycles, and essential role in Nature, have attracted the attention of naturalists, biologists, geneticists, ecologists, chemists, and biochemists in myriad ways over many years. Understandably, knowledge of the fungal world developed as areas of specialization that interdigitated with one another loosely, if at all. Molecular biology has put more of the fungal world within experimental reach, but more importantly, it is permitting us to make connections where the parochial views of individual sub-disciplines had prevailed. It is allowing us rapidly to gain at least a rudimentary appreciation of some universal cellular mechanisms at work within the fungal realm. Our aim with this book project was to gather expert contributing authors whose chapters collectively would be more than a snapshot of the biotechnology of filamentous fungi today; we hoped that their chapters would vividly illustrate the unifying force that molecular genetics has become in fungal biology and technology. As the book was readied for publication, we were pleased to see that the authors have, to a large extent, achieved this goal and have gone on to provide glimpses of where our new techniques and insights may allow us to venture in the near future. As we view fungi in relation to the biological world in its entirety, another contribu­ tion of molecular genetics becomes apparent in the compelling evidence that the fungal kingdom is related more closely to animals than to plants. Recently we have been reminded that man's relationship with fungi extends over a very long period of history: the 5000-year-old "Ice Man" found in a receding Tyrolean glacier in 1991 carried mycelia of Fomes fomentarius in a leather pouch and tissue of the bracket fungus, Piptoporus betulinus, purposefully strung on a leather strap. Yet the modem view of phylogeny points to a biological relatedness between man and fungi extending back over many more millennia. For evidence of this shared heritage we need only consider the magnitude of the challenge inherent in developing non-toxic and selective agents to fight the life-threatening human mycoses that are increasing in prevalence as populations of immunosuppressed patients expand. For mycology, the analysis of divergence in selected DNA sequences has generally affirmed the conventional, morphologically-based taxonomical classification . However,

xix xx Preface it has also revealed strikingly surprising relationships and exposed artificial assemblages of anamorphs, as well. Discussions and disputes about various species concepts (taxonomi­ cal, biological, phylogenetic, or ecological) are likely to continue for years to come. Very importantly for the applied aspects of mycology, a phylogeny based on DNA divergence provides the framework for the facile identification of new isolates, especially strains known only in their anamorphic state. Genomic sequencing has been completed for a few filamentous fungi, and some general conclusions are emerging. However, a significant portion of the sequence data has not been widely available, having been generated by commercial entities intent upon utilizing the information in the development of agricultural fungicides or therapeutic agents for human and animal health. Soon, ongoing international academic sequencing initiatives will increase significantly the number of sequenced fungal genomes in the pub­ lic domain. Gleaning information from this mass of new data will likely require an effort in the next decade approximating that expended acquiring the data over the last 10 years. It will call for the development or improvement of bioinformatics tools and user-friendly platforms that will allow convenient and reliable annotation of the fungal open reading frames (ORFs) and offer the possibility of conducting comparative genomic inquiries more expediently. To verify provisional annotations and deepen the understanding of given ORFs, techniques for functional genomic analyses that can be applied globally, or at least in a high throughput mode, will need to be implemented. The point of departure for this book is a series of chapters on modern fungal systematics, genomics, and genetic tools for functional analysis. Grouped under the heading of Genetic Technology, they set the stage for the subsequent chapters that are organized into three additional groups. The two sections at the heart of the book are devoted to the economic impacts of fungi. (Though yeasts are, of course, fungi and have a long history of use in biotechnol­ ogy, we asked the chapter authors to focus specifically upon the filamentous fungi, rather than their well-studied cousins.) Today a wide range of industries make use of filamentous fungi or their products. Fungal organisms are also increasingly employed for waste treat­ ment and bioremediation. Biotechnology can trace its historical roots to the use of microorganisms in the production and processing of beverages and foods, and the value of filamentous fungi in some of these processes was undoubtedly recognized in antiquity. Modern-day palates are quite familiar with the flavors, textures, and metabolites provided by filamentous fungi in cheeses, oriental sauces, and other food products . The submerged fermentation processes developed near the middle of the past century for citric acid and penicillin production by filamentous fungi are still paradigms for the production aspects of modern biotechnology. In recent decades the commercial value of filamentous fungi has grown as they have become important sources of pharmaceutical agents for the treatment of infectious and metabolic diseases and of a broad range of enzymes used to process foods and animal feeds, fortify detergents, treat textiles and wood pulp by-products , and perform highly specific biotransformations. Today the commercial goods produced by industries that make use of fungi represent a segment of the world economy valued in billions of dollars annually. Despite the variety of ways that fungi provide economic benefits to mankind, their most significant economic impact is measured in terms of losses, especially agricultural losses. Molds are widespread pathogens of crop plants, they are agents of food spoilage and deterioration, and they are responsible for the contamination of grains with toxic and, Preface xxi in some instances, carcinogenic compounds. Although we humans tend to view their activities as favorable or damaging in economic terms, for the fungus there is no dichotomy. The ability to make a special metabolite that is not part of general metabolism, whether the metabolite is a potent carcinogen or an inhibitor of sterol synthesis that can be beneficial in the management of serum cholesterol levels, is for the fungus simply an evolutionary adaptation , perhaps of utility in exploiting and inhabiting a specific natural niche. Similarly enzymes that enable fungi to play their crucial role as Nature 's recyclers are also the ones that degrade our wooden structures or that can be used to improve the nutritional value of animal feed. In the discussion of genomic structure in Chapter 2, one is struck with the realization that genes found uniquely in fungi are, for the most part, the very ones that mediate processes with economic consequences. Thus, the chapters related to special metabolites (traditionally known as secondary metabolites) that comprise the second section of the book, treat their subjects in biosyn­ thetic terms rather than from the perspective of positive or negative consequences in human affairs. The three major classes of fungal special metabolites are considered: polyketides derived from acetate equivalents, non-ribosomal peptides made from amino and hydroxy acids, and isoprenoids, also known as terpenes, that arise from isoprenyl units. The enzymes necessary to produce members of each class are encoded by genes that are carried in the genome principally as clusters , and at least for polyketides, it is clear that one organism may retain several clusters for different products. Considering the significant proportion of genomic DNA devoted to these clusters as well as the conservation of func­ tional clusters in wild strains and in unrelated members of the fungal kingdom, one can clearly appreciate just how misleading it is to consider special metabolites as secondary or dispensable. The theme of evolutionary adaptation continues in the third section of the book that is devoted to enzymes produced by fungi. Here the metabolic versatility of fungi is in the limelight as the chapters explore the wide-ranging uses that have been found for fungal enzymes. Through molecular technology, the selection of proteins produced commercially in fungi has been broadened to include enzymes of plants, animals, and humans, and strategies have been developed to tailor the characteristics of an enzyme to meet the needs of a specific industrial or agricultural process. Also to be found in this section are exam­ ples of fungal cells exploited as biocatalysts to transform synthetic organic substrates selectively and stereospecifically or to convert a common or inexpensive precursor into a product with commercial value. Interest in biocatalysis is high in the fine chemicals industry that is faced with the need to minimize production and energy costs and any negative environmental consequences of its large-scale processes. Biocatalysis is also receiving increasing attention for its potential in environmental remediation. The chapters in this third section are grouped under the heading of Enzymes and Green Chemistry. The last section of the book, with three chapters under the heading Host-Fungal Interactions, returns the perspective to the level of the organism to illustrate how the unique capabilities of fungi, discussed in genomic, enzymatic , and chemical terms in earlier portions of the book, translate into the success of the whole organism, as a pathogen or symbiont. At the conclusion the chapters leave us standing on the threshold of an era of "func­ tional genomic s" which promises to provide an appreciation of the complexity of cellular processes that could not have been attained previously. The limitations of linearity in xxii Preface conceptualization and experimental approaches, exemplified by the 'one gene, one protein, one function' mind-set, are giving way as networks of metabolic and regulatory functions are revealed. Here biotechnology may have an opportunity to repay a portion of its debt to basic science through its well-developed mathematics and algorithms for principal com­ ponent analysis and multivariable analyses that are widely used in the development of industrial fermentation processes. We may also expect the next decade to bring a wider appreciation of the regulatory implications and metabolic consequences (metabolite chan­ neling) of protein/protein interactions. Multiple functions for a single gene product are likely to come to light. Already today a variety of new fluorescent probes and imaging techniques make it possible to determine the subcellular location of a specific protein throughout the division cycle, and these methods should become a standard part of the characterization of a gene product in the future. For fungal biotechnology, new doors are opening allowing consideration of strate­ gies not previously feasible. Gene homologs can be sought in a collection of organisms to identify species capable of more robust production of the gene product or to provide DNA sequence information for the design of a 'consensus' protein (see Chapter 10). Segments of gene homologs from several organisms can be shuffled to identify products with improved characteristics. Although information of this kind will increasingly be available by comparative genomics, it can also be obtained with DNA extracted from a natural habi­ tat, without ever isolating the organisms present in that habitat. It may become possible to circumvent the bottleneck that the random mutation approach has represented in strain improvement and process development by utilizing rational strategies. For example, a clus­ ter of genes or, perhaps, a key gene from a cluster, may be moved into an organism that already has favorable characteristics for growth in large-scale fermentor tanks or has already proven amenable to the efficient production or secretion of the type of product desired. As an alternative or adjunct, genes derived from global signaling cascades and reg­ ulatory circuits bearing mutations making their products functionally dominant can be introduced into the producing organism to deregulate metabolite synthesis. Deregulation via this approach could also prove useful in assessing the full potential of a new isolate to produce bioactive compounds . For fungal strains that have already been engineered to improve the efficiency of protein folding and secretion, it may soon prove feasible to alter their glycosylation pathways to produce mammalian-type oligosaccharides, a development which could make fungal fermentation a realistic alternative to mammalian cell culture for the production of therapeutic glycoproteins such as antibodies. With new possibilities such as these, fungal biotechnology will surely continue to flourish. Thirty-nine authors from laboratories around the world prepared chapters for this book, and we conclude this introduction by expressing our gratitude to them for the time and effort they generously contributed . Our hope would be that their texts will help attract, train, and inspire a new generation of scientists who will advance the field of mycology that we find a continual source of fascination. Jan S. Tkacz Lene Lange