Fungi Fungi Biology and Applications Editor Kevin Kavanagh Department of Biology National University of Ireland Maynooth Co Kildare Ireland Copyright © 2005 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England Telephone (+44) 1243 779777 Email (for orders and customer service enquiries): cs-books@wiley.co.uk Visit our Home Page on www.wileyeurope.com or www.wiley.com 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, scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 or under the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1T 4LP, UK, without the permission in writing of the Publisher Requests to the Publisher should be addressed to the Permissions Department, John Wiley & Sons Ltd, The Atrium, Southern Gate, 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Some content that appears in print may not be available in electronic books Library of Congress Cataloging-in-Publication Data Fungi : biology and applications / editor, Kevin Kavanagh p ; cm Includes bibliographical references and index ISBN 0-470-86701-9 (hb : alk paper) — ISBN 0-470-86702-7 (pb : alk paper) Fungi—Biotechnology Fungi [DNLM: Fungi Biotechnology QW 180 F981 2005] I Kavanagh, Kevin TP248.27.F86F875 579.5—dc22 2005 2004029635 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN 0-470-86701-9 (HB) 0-470-86702-7 (PB) Typeset in 10.5/13pt Sabon by SNP Best-set Typesetter Ltd., Hong Kong Printed and bound in Great Britain by Antony Rowe, Ltd, Chippenham, Wiltshire This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production Contents List of Contributors ix Preface xi 1 Introduction to Fungal Physiology Graeme M Walker and Nia A White 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2 10 22 26 34 34 34 Fungal Genetics Malcolm Whiteway and Catherine Bachewich 35 2.1 2.2 2.3 2.4 35 37 43 2.5 2.6 2.7 2.8 Introduction Morphology of yeasts and fungi Ultrastructure and function of fungal cells Fungal nutrition and cellular biosyntheses Fungal metabolism Fungal growth and reproduction Conclusions Further reading Revision questions Introduction Fungal life cycles Sexual analysis: regulation of mating Unique characteristics of filamentous fungi that are advantageous for genetic analysis Genetics as a tool Conclusions Further reading Revision questions 49 50 61 62 62 Fungal Genetics: A Post-Genomic Perspective Brendan Curran and Virginia Bugeja 65 3.1 3.2 65 66 Introduction Genomics vi CONTENTS 3.3 3.4 3.5 3.6 3.7 3.8 Fungal Fermentation Systems and Products Kevin Kavanagh 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 Introduction Fungal fermentation systems Ethanol production Commercial fungal products Genetic manipulation of fungi Conclusion Further reading Revision questions Antibiotics, Enzymes and Chemical Commodities from Fungi Richard A Murphy and Karina A Horgan 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 5.10 Transcriptomics and proteomics Proteomics Systems biology Conclusions Further reading Revision questions Introduction Fungal metabolism Antibiotic production Pharmacologically active products Enzymes Chemical commodities Yeast extracts Enriched yeast Further reading Revision questions The Biotechnological Exploitation of Heterologous Protein Production in Fungi Brendan Curran and Virginia Bugeja 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 Fungal biotechnology Heterologous protein expression in fungi Budding stars Methylotrophic yeast species Case study – hepatitis B vaccine – a billion dollar heterologous protein from yeast Further biotechnological applications of expression technology Conclusion Further reading Revision questions 75 80 85 87 87 88 89 89 90 96 101 108 111 111 111 113 113 113 116 123 125 129 138 140 142 143 145 145 146 149 155 158 163 168 168 169 CONTENTS Fungal Diseases of Humans Derek Sullivan, Gary Moran and David Coleman 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 Antifungal Agents for Use in Human Therapy Khaled H Abu-Elteen and Mawieh Hamad 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 8.10 Introduction Fungal diseases Superficial mycoses Opportunistic mycoses Endemic systemic mycoses Concluding remarks Further reading Revision questions Introduction Polyene antifungal agents The azole antifungal agents Flucytosine Novel antifungal agents Miscellaneous antifungal agents New strategies and future prospects Conclusion Further reading Revision questions Fungal Pathogens of Plants Fiona Doohan 9.1 9.2 9.3 9.4 9.5 9.6 9.7 9.8 9.9 9.10 9.11 9.12 9.13 9.14 9.15 9.16 9.17 9.18 9.19 Fungal pathogens of plants Disease symptoms Factors influencing disease development The disease cycle Genetics of the plant–fungal pathogen interaction Mechanisms of fungal plant parasitism Mechanisms of host defence Disease control Disease detection and diagnosis Vascular wilt diseases Blights Rots and damping-off diseases Leaf and stem spots, anthracnose and scabs Rusts, smuts and powdery mildew diseases Global repercussions of fungal diseases of plants Conclusion Acknowledgements Further reading Revision questions Answers to Revision Questions Chapter Chapter vii 171 171 172 172 173 186 189 189 190 191 191 192 197 204 207 210 214 216 216 217 219 219 220 224 225 226 227 231 233 236 238 242 244 246 247 248 249 249 249 250 251 251 252 viii CONTENTS Chapter Chapter Chapter Chapter Chapter Chapter Chapter Index 253 256 257 258 260 261 261 263 List of Contributors Dr Khaled H Abu-Elteen, Department of Biological Science, Hashemite University, Zarqa 13133, Jordan Dr Catherine Bachewich, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, Canada H4P 2R2 Dr Virginia Bugeja, School of Natural Sciences, University of Hertfordshire, College Lane, Hatfield, Hertfordshire AL10 9AB, UK Prof David Coleman, Microbiology Research Laboratory, Dublin Dental Hospital, Trinity College, Dublin 2, Ireland Dr Brendan Curran, School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK Dr Fiona Doohan, Department of Plant Pathology, University College Dublin, Belfield, Dublin 4, Ireland Dr Mawieh Hamad, Department of Biological Science, Hashemite University, Zarqa 13133, Jordan Dr Karina A Horgan, Alltech Biotechnology Centre, Summerhill Road, Dunboyne, Co Meath, Ireland Dr Kevin Kavanagh, Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland Dr Gary Moran, Microbiology Research Laboratory, Dublin Dental Hospital, Trinity College, Dublin 2, Ireland Dr Richard A Murphy, Alltech Biotechnology Centre, Summerhill Road, Dunboyne, Co Meath, Ireland 266 INDEX Microarrays 76, 79 Microfungi 2, Morpholines 209 Mutagenesis 108 Mycetoma 173 Mycoprotein 90, 102–104 Mycotoxins 187–189, 248, 249 Powdery mildew 247 Programmed cell death 32, 46 Protease(s) 126, 149, 152, 229 Proteomics 65, 75, 80 Protoperithecia 41 Protoplast 5, 54 Pseudohyphae 28 Neurospora 5, 35, 38, 46, 52, 75 Nitrogen 12, 13 Nitrogen metabolism 25–26 Northern Blot 75 Nystatin 192–197 Quorn mycoprotein 17, 102–104 Oak Wilt Disease 242 Octenidine 209 Ooligotrophic 11 Open reading frame (ORF) 69, 70, 74, 84 Opportunistic infection 172 Pachysolen tannophilus 92 Parasexual analysis 49 Parasitism 219 Penicillin 90, 104, 108 binding protein (PBP) 117 Penicillium chrysogenum 104 Penicillium notatum 104 Pentose sugars 24 Peptide fragments 81 pH (effect on growth) 27 Phaffia rhodozyma Pheromone 41, 46 Phosphorous 13 Phythopthora infestans 90, 221, 242–244 Phytium damping-off disease 244–245 Pichia pastoris expression system 156 Pirtenidine 209 Pityriasis versicolor 172 Plant diseases (symptoms) 220 Plasma membrane 19 Plasmid (2m) 55 Pneumocystis pneumonia (PCP) 185 Polyene antifungals 192–197 Mechanism of action of polyenes 194–196 Pharmacokinetics of polyenes 196 Properties of polyenes 192–194 Resistance to polyenes 196–197 Spectrum of activity of polyenes 196 Population growth 30–32 Potato blight 90, 242–244 Random spore analysis 514 Rare mating 108 Recombinant vaccine 161 Reproduction (cellular) 28–30 Resistance (R) genes 227, 231 Respiration (Alternative) 25 Respiration (Normal) 25 Reverse genetics 71–74 Rhizomorphs Rhodotorula rubra Riboflavin 136 Ringworm 173 Rusts 247 Saccharomyces cerevisiae 2, 36–38, 150 Saccharomycopsis 102 Saprophytism 219 Scabs 246 Scale-up (fermentation) 122 Schizosaccharomyces pombe 36, 46, 74 Selected tetrads 51 Selenium yeast 141 Single cell protein (SCP) 102–104 Smuts 247 Solid fermentation 91 Sordarins 211 Sphaeroplasts 149 Spitzenkorper 10 Starch 97, 126 Statins 123, 166 Stationary phase 31 Sulphur 13 Superficial infections 172–173 Symbiosis 219 Synthetic genetic arrays (SGA) 52 Systemic infections 171 Systems Biology 65, 85–86 Temperature (effect on growth) 26, 27 Tetrad analysis 50 Thiocarbamate(s) 208 Tinea 173 INDEX Tinea nigra 172 Toxins (fungal) 187–188, 229–230, 248 Aflatoxin B1 188 K1 toxin 33 Mycotoxins 187–189, 248, 249 T-2 toxin 249 Transcriptomics 66, 75, 77, 79 Transformation 54, 109, 148–149 Transport 20 Trehalose 21 Tubulin 59 Uridine Biosynthesis pathway 55 UTH (youth) genes 33 Vaccines: Antifungal: 215 Hepatitis B: 158–163 Recombinant vaccine 161 Vascular Wilt Diseases 238 Vectors 36 Verticillium 107 Verticillium wilt 240–241 Vitamin B2 136 Vitamin D 137 267 Vitamins 18, 135–138 Industrial production 135–138 Vulvo-vaginal candidosis 176 Water activity (aw) 27, 91 Whie-rot fungi 23 Woronin bodies Wort 98 Xylose fermentation 93, 109 Yeast Aureobasidium pullans Budding yeast 3, 28, 29 Candida albicans 5, 47, 68, 73, 79, 175 Candida dubliniensis 73, 175 Candida spp 174 Cryptococcus 4, 5, 42, 47, 185, 196 Geotrichum candidum Histoplasma capsulatum 73 Pachysolen tannophilus 92 Saccharomyces cerevisiae 2, 36–38, 150 Saccharomycopsis 102 Schizosaccharomyces pombe 36, 46, 74 Selenium yeast 141 Yeast extract 138–140 (i) (j) (k) (l) (g) (m) (a) (b) (c) (d) (h) (e) (f) Plate 1MRadiating circular pattern of (a) Chlorophyllum molybdites fruit-bodies forming a fairy ring in grassland and (b) Tinea corporis infection of the skin (c) Fruiting bodies of Agaricus bitorquis, (d) scanning electron micrograph of Agaricus bisporus gill surface (P.T Atkey), (e) light micrograph of basidium bearing two spores (T.J Elliott), (f) spore print from underside of fruitbody (M.P Callen), (g) germ-tubes emerging from spores (T.J Elliott; published by John Wiley & Sons, Ltd), (h) branching hyphae growing on an agar plate (T.J Elliott) (all from Carlile, Watkinson and Gooday (2001) Academic Press) The dry-rot fungus Serpula lacrymans (i) colony decaying timbers in a wall void and forming a red-brown fruiting structure, (j) close-up of underside of a basidiocarp (from Ingold and Hudson, published by Chapman & Hall, Ltd), (k) exploratory fan-shaped mycelium with connected rhizomorphs, (l) fast- and (m) slow-growing colonies growing on agar media Plate 2MTwo-colour microarray technology 6400 distinct ORFs are arrayed on the slide (only 36 are shown here) Two separate cDNA samples, one from yeast growing in glucose at the beginning of the fermentation labeled with a green fluorescent dye and the other from later in the fermentation labelled with the red dye Red colour indicates gene expression increased relative to the reference, green colour indicates gene expression decreased relative to the reference and yellow colour indicates no change in expression level Three ORFs are shown in detail here Plate 3MPattern interpretation of microarray (after deRisi et al., 1997) This shows how the expression levels of genes known to be stress-induced via STREs in their promoters were identical to one another (The promoter sequences of other genes with the same profile but not previously identified as stress-inducible were then examined – many contain one or more recognizable STRE sites.) Plate 4MA photograph of the oral cavity of a patient with pseudomembranous oral candidosis (thrush) Plate 5MA photograph of a CHROMagar CandidaTM plate on which a variety of Candida species have been cultured Note that most species can be differentiated on the basis of the colour of the colonies produced (1) (2) (3) (4) Plate 6MA schematic diagram indicating the stages of candidal infection Plate 7MVariation in the head blight susceptibility of two barley cultivars to Fusarium head blight disease Both heads were inoculated with Fusarium culmorum, but only the cultivar on the left shows disease symptoms (premature bleaching of head spikelets) (a) (b) Plate 8MEffect of deoxynivalenol, a non-host-specific fungal trichothecene toxin, on the germination of wheat seedlings Seeds germinated on toxin solution (a) show reduced root and coleoptile growth compared with those germinated on water (b) Plate 9MClubroot of brassicas caused by Plasmodiophora brassicae Roots swell and develop tumours due to increased hormone (e.g cytokinin) production (a) (b) Plate 10MBiological control of net blotch disease of barley (caused by Perenophora teres) by a bacteria (Bacillus spp.) originating from a cereal field The blotch disease symptom severity caused by this pathogen on inoculated leaves in the absence (a) and presence (b) of the biocontrol agent (a) (b) (c) Plate 11MFusarium wilt Microscopic analysis of typical asexual macroconidia (a) and mycelial growth on potato dextrose agar (b) of Fusarium species (Fusarium oxysporum also produces microconidia and chlamydospores) (c) Fusarium oxysporum f sp lycopersici wilt of tomato: symptoms range from healthy (left) to severe wilting and stunting (right) (courtesy Dr Antonio Di Pietro, Cordoba, Spain: Di Petro et al., 2003) Plate 12MYellowing/browning of leaves of an elm branch due to Dutch elm disease The entire tree subsequently wilted and died (a) (c) (b) (d) Plate 13MPhytophthora infestans late blight of potatoes Microscopic analysis of asexual sporangia containing zoospores (a) and sexual oospore (b) Disease symptoms: water-soaked dark lesions on leaves (c) and diseased tubers exhibit brown/black blotches on their surface, and internally, they exhibit water-soaked dark-brown rotted tissue (d) (a) (c) (b) Plate 14MPythium damping-off disease (a) Asexual sporangia containing zoospores; (b) sexually-produced oospore formed on the surface of a tomato seedling; (c) seedlings of cress that are healthy (left) and others exhibiting damping-off symptoms (right) (a) (b) Plate 15MSeptoria leaf blotch of wheat caused by Mycosphaerella graminicola (a) Oval disease lesions (surrounded by a chlorotic halo) on an infected leaf, running parallel to the leaf blade; (b) black pycnidia develop on mature lesions and cirri may form on the lesions if the weather is dry for prolonged periods Plate 16MSunken lesions on broad-bean pod due to anthracnose disease caused by Colletotrichum lindemuthianum Plate 17MBlack stem rust of mature wheat stems caused by Puccinia graminis f sp tritici The three stems possess black pustules of teliospores; these pustules arise from red urediospore pustules that erupt through the stem epidermis earlier in the growing season (a) (b) Plate 18MSmut diseases of cereals Covered smut of oats caused by Ustilago hordei (a) and covered smut or ‘bunt’ of wheat caused by Tilletia species (b) Grain are replaced with black spore masses and hence destroyed Plate 19MPowdery mildew disease of wheat caused by Blumeria (=Erysiphae) graminis Symptoms of powdery mildew disease include chlorotic or necrotic leaves, and stems and fruits covered with mycelium and fruiting bodies of the fungus, often giving a white ‘woolly’ appearance ...Fungi Fungi Biology and Applications Editor Kevin Kavanagh Department of Biology National University of Ireland Maynooth Co Kildare Ireland Copyright © 2005 John Wiley &... given an up-to-date and detailed account of our knowledge of the biology and various applications of fungi Kevin Kavanagh Introduction to Fungal Physiology Graeme M Walker and Nia A White 1.1... Jordan Dr Karina A Horgan, Alltech Biotechnology Centre, Summerhill Road, Dunboyne, Co Meath, Ireland Dr Kevin Kavanagh, Department of Biology, National University of Ireland, Maynooth, Co Kildare,