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Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine Advances in Fungal Biotechnology for Industry, Agriculture, and Medicine 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 A C.I.P. record for this book is available from the Library of Congress All rights reserved No part of this book may be reproduced, stored in a retrieva! system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming. recording. or otherwise. without written permis sion from the Publisher. with the exception of an)' material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Permissions for books published in Europe: [email protected] Permissions for books published in the United States of America: [email protected] Contributors 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.
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