Fungi Fungi Biology and Applications Third Edition Edited by Kevin Kavanagh Department of Biology Maynooth University Maynooth County Kildare Ireland This edition first published 2018 © 2018 John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or other- wise, except as permitted by law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions. The right of Kevin Kavanagh to be identified as the author of the editorial material in this work has been asserted in accordance with law. Registered Office(s) John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA Editorial Office 111 River Street, Hoboken, NJ 07030, USA For details of our global editorial offices, customer services, and more information about Wiley products visit us at www.wiley.com. 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Other titles: Fungi (Kavanagh) Description: Third edition. | Hoboken, NJ : Wiley, 2017. | Includes bibliographical references and index. | Identifiers: LCCN 2017032708 (print) | LCCN 2017033915 (ebook) | ISBN 9781119374169 (ePDF) | ISBN 9781119374275 (ePUB) | ISBN 9781119374329 (paperback) Subjects: | MESH: Fungi | Biotechnology Classification: LCC TP248.27.F86 (ebook) | LCCTP248.27.F86 (print) | NLM QW 180 | DDC 579.5–dc23 LC record available at https://lccn.loc.gov/2017032708 Cover design: Wiley Cover image: (Background) © Anna_Gavrylova/Gettyimages; (Chemical Structures) © chromatos/Shutterstock Set in 10.5/13pt Sabon by SPi Global, Pondicherry, India 10 9 8 7 6 5 4 3 2 1 Contents List of Contributors ix Preface xi 1 Introduction to Fungal Physiology 1 Graeme M. Walker and Nia A. White 1.1 Introduction 1 1.2 Morphology of Yeasts and Fungi 2 1.3 Ultrastructure and Function of Fungal Cells 5 1.4 Fungal Nutrition and Cellular Biosyntheses 11 1.5 Fungal Metabolism 22 1.6 Fungal Growth and Reproduction 26 1.7 Conclusion 34 Further Reading 34 2 Fungal Genetics 37 Malcolm Whiteway and Catherine Bachewich 2.1 Introduction 37 2.2 Fungal Lifecycles 39 2.3 Sexual Analysis: Regulation of Mating 46 2.4 Unique Characteristics of Filamentous Fungi that Are Advantageous for Genetic Analysis 51 2.5 Genetics as a Tool 52 2.6 Conclusion 64 Acknowledgment 65 Further Reading 65 3 Fungal Genomics 67 David Fitzpatrick 3.1 Introduction 67 3.2 Genome Sequencing 70 vi CONTENTS 3.3 Bioinformatics Tools 75 3.4 Comparative Genomics 80 3.5 Genomics and the Fungal Tree of Life 84 3.6 Online Fungal Genomic Resources 86 3.7 Conclusion 88 Further Reading 88 4 Fungal Genetics: A Post‐Genomic Perspective 91 Brendan Curran and Virginia Bugeja 4.1 Introduction 91 4.2 The Yeast Saccharomyces cerevisiae: A Cornerstone of Post‐Genomic Research 91 4.3 Of ‐omics and Systems Biology 92 4.4 Genomics 92 4.5 Transcriptomics and Proteomics 102 4.6 Systems Biology 115 4.7 Conclusion 117 Further Reading 117 5 Fungal Proteomics 119 Sean Doyle and Rebecca A. Owens 5.1 Introduction 119 5.2 Protein Isolation and Purification 121 5.3 Electrophoretic Techniques 126 5.4 Protein Mass Spectrometry 129 5.5 Fungal Proteomics 138 5.6 Label‐Free Quantitative Proteomic Applications 143 5.7 Specialized Proteomics Applications in Fungal Research 144 5.8 Conclusion 145 Acknowledgments 145 Further Reading 145 6 Fungi as Food 147 Johan Baars 6.1 Introduction 147 6.2 The Main Cultivated Mushroom Species 149 6.3 The Main Species of Mushroom Collected in Nature 155 6.4 Nutritional Value of Mushrooms 159 6.5 Potential Medicinal Properties of Mushrooms 165 6.6 Conclusion 166 Further Reading 167 Useful Websites 168 7 Pharmaceutical and Chemical Commodities from Fungi 169 Karina A. Horgan and Richard A. Murphy 7.1 Introduction 169 7.2 Fungal Metabolism 169 7.3 Antibiotic Production 172 7.4 Pharmacologically Active Compounds 178 7.5 Chemical Commodities 184 7.6 Yeast Extracts 194 CONTENTS vii 7.7 Enriched Yeast 196 7.8 Conclusion 198 Further Reading 198 8 Biotechnological Use of Fungal Enzymes 201 Shauna M. McKelvey and Richard A. Murphy 8.1 Introduction 201 8.2 Enzymes in Industry 202 8.3 Current Enzyme Applications 202 8.4 Enzymes and Sustainability 208 8.5 Future Direction of Industrial Enzymes 208 8.6 Applications of Specific Fungal Enzymes 208 8.7 Enzyme Production Strategies 223 8.8 Conclusion 224 Further Reading 225 9 Biotechnological Exploitation of Heterologous Protein Production in Fungi 227 Brendan Curran and Virginia Bugeja 9.1 Introduction 227 9.2 Heterologous Protein Expression in Fungi 228 9.3 Use of Saccharomyces cerevisiae for Heterologous Protein Production 232 9.4 Use of Pichia pastoris for Heterologous Protein Production 238 9.5 Case Study: Hepatitis B Vaccine – A Billion‐Dollar Heterologous Protein from Yeast 240 9.6 Further Biotechnological Applications of Expression Technology 244 9.7 Conclusion 248 Further Reading 249 10 Fungal Infections of Humans 251 Derek J. Sullivan, Gary P. Moran, and David C. Coleman 10.1 Introduction 251 10.2 Superficial Mycoses 252 10.3 Opportunistic Mycoses 254 10.4 Endemic Systemic Mycoses 268 10.5 Mycotoxicoses 270 10.6 Conclusion 271 Further Reading 272 Useful Websites 273 11 Immunity to Human Fungal Infections 275 Mawieh Hamad, Mohammad G. Mohammad, and Khaled H. Abu‐Elteen 11.1 Introduction 275 11.2 Compromised Immunity Increases Host Susceptibility to Fungal Infections 276 11.3 Shaping of the Antifungal Immune Response 277 11.4 Paradigm Shifts in Antifungal Immunity 281 11.5 Anatomy of the Antifungal Immune Response 283 11.6 The Role of DCs in Antifungal Immunity 288 viii CONTENTS 11.7 Adaptive Immunity to Fungal Infections 290 11.8 Immunity to Dermatophytes 295 11.9 Evasion of Host Immunity by Fungal Pathogens 297 11.10 Conclusion 297 Further Reading 298 12 Antifungal Agents for Use in Human Therapy 299 Khaled H. Abu‐Elteen and Mawieh Hamad 12.1 Introduction 299 12.2 Drugs Targeting the Plasma Membrane 303 12.3 Drugs Targeting the Cell Wall 319 12.4 Drugs Targeting Nucleic Acid and Protein Synthesis 323 12.5 Novel Therapies 327 12.6 Conclusion 331 Further Reading 331 13 Fungi in the Environment 333 Richard O’Hanlon 13.1 Introduction 333 13.2 Macrofungi, Mushrooms, and Sporocarps 334 13.3 Symbiotic Fungi 336 13.4 Saprobic Fungi 339 13.5 Parasitic Fungi 341 13.6 Fungi in Food Webs 342 13.7 Fungi and Nutrient Cycling 344 13.8 Quantifying Fungi in the Environment 346 13.9 Conclusion 352 Further Reading 353 14 Fungal Pathogens of Plants 355 Fiona Doohan and Binbin Zhou 14.1 Introduction 355 14.2 Disease Symptoms 356 14.3 Factors Influencing Disease Development 356 14.4 The Disease Cycle 361 14.5 Genetics of the Plant–Fungal Pathogen Interaction 363 14.6 Mechanisms of Fungal Plant Parasitism 363 14.7 Mechanisms of Host Defense 367 14.8 Disease Control 369 14.9 Disease Detection and Diagnosis 373 14.10 Vascular Wilt Diseases 374 14.11 Blights 378 14.12 Rots and Damping‐Off Diseases 380 14.13 Leaf and Stem Spots, Anthracnose, and Scabs 382 14.14 Rusts, Smuts, and Powdery Mildew Diseases 383 14.15 Global Repercussions of Fungal Diseases of Plants 384 14.16 Conclusion 385 Acknowledgments 386 Further Reading 386 Index 389 List of Contributors Professor Khaled H. Abu‐Elteen, Department of Biological Science, Hashemite University, Zarqa, Jordan. Dr Johan Baars, Plant Research International, Wageningen, The Netherlands. Professor Catherine Bachewich, Department of Biology, Concordia University, Montreal, Canada. Dr Virginia Bugeja, School of Life Sciences, University of Hertfordshire, Hatfield, Hertfordshire, UK.