Qk603m34 2005

579.5--dc22 2005041276

fH3 informa

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Dedicated to Manjuli and Govind

Preface

Fungi are organisms generally composed of tubes that are invisible to the naked eye. The cells of these tubes are multinucleate and in cytoplasmic continuity. Fungi are among the oldest and largest living organisms, rivaling the mass of a California redwood tree or a blue whale. As the chief agents of decomposition of organic matter, fungi contribute to the sustenance of the carbon cycle. As mycorrhizal partners of roots, they provide the primary mechanism for the capture of nutrients used by plants, thereby contributing to the green cover on earth. Some fungi occur as endophytes in plants or as symbiotic partners with algae, allowing the mutualistic partners to tolerate and grow in harsh conditions that they could not do otherwise. As virulent pathogens of plants, fungi are a constant threat in agriculture and forestry. Since antiquity, fungus has been exploited either unwittingly or intentionally for the conversion of grape juice into ethanol in wine. As producers of antibacterial compounds, fungi are sources of life-saving drugs. They are the only eukaryotic organisms that can thrive at temperatures beyond which no plant or animal can live. Though potentially immortal, a few fungi have a limited life span, providing valuable models for investigating the mechanisms in aging and death. Fungi are now at the forefront of research on mechanisms in gene silencing, biological rhythm, mating processes, biogenesis of intracellular organelles, adaptations to hostile habitats, structure of natural populations and speciation. Because of their small genomes, fungi are being used in "systems biology" to understand the connections between genes, proteins, metabolic and signaling pathways.

This book on fungi is an outcome of my association with graduate students in biochemistry. The majority of these students had little or no previous exposure to fungi and a few not even to biology. I found that students became interested in fungi if an attempt was made to demonstrate fungi in natural situations and how they could be used to understand complex biological questions, in particular if the design of the experiments that were done to obtain information were described. Today's accelerated pace of research, aided by new instruments and techniques combining the approaches of genetics, biochemistry and cell biology, has changed the character of mycology, necessitating a new approach for the organization of the subject matter and learning about the fungi.

This book should be useful both for a beginning research worker and a professional. The subject matter is divided into six parts, comprising 14 chapters. Each chapter is self-contained and written in a style that enables the reader to progress from elementary concepts to current thinking on a topic. Throughout, attention is drawn to unsolved questions. References are given only to selected publications, primarily for details on the design of experiments that were used to obtain information, and for the identification of some of the key players. Finally, an Appendix gives the principles in naming fungi, estimated to comprise more than 1.5 million species, and of their broad classification. Many authors include the slime molds in the fungi. Since they consist of naked cells, move in amoeboid fashion and ingest particulate food, I have excluded them.

Ramesh Maheshwari

September 2004

Acknowledgments

I express my gratitude to those who kindled, guided, or stimulated my interest in fungi. My father, Professor Panchanan Maheshwari FRS (University of Delhi), introduced me to fungi and guided my pre-doctoral research on the life history of a subtropical rust fungus. My Ph.D. research supervisors, Professors Paul J. Allen and Albert C. Hildebrandt (University of Wisconsin), and my postdoctoral mentors, Professors Alfred S. Sussman (University of Michigan) and David D. Perkins (Stanford University), deepened my knowledge of fungi. David Perkins encouraged me to write this book by giving invaluable suggestions and answering questions through electronic mail. Dr. Namboori B. Raju (Stanford University) and Professor Rowland H. Davis (University of California, Irvine) also answered several queries. Among my former graduate students, Dr. Mahalingeshwara K. Bhat (Norwich) regularly sent me photocopies of several publications and Dr. Amitabha Chaudhuri (Connecticut) contributed Chapter 6. K. Pitchaimani, Kamal Dev and Anthony D'Souza helped to finalize the contents of the book from the viewpoint of graduate students. Kamal Dev scanned published figures, made some new figures and gave much computer assistance. I am indebted to Dr. Keyur K. Adhvaryu, Dr. M.K. Bhat, Dr. Gagan D. Gupta, Dr. Gordon E. Holcomb, Dr. David J. Jacobson, Dr. Durgadas P. Kasbekar, Dr. Martha Merrow and Dr. Namboori B. Raju, who read and commented on some chapters. My wife, Manjuli, helped me cope with my recent physical disability and minimized the gestation period by reading all chapters and making corrections to improve the text. My brother-in-law Arvind Gupta and my son Govind also helped in ways that enabled writing to be completed. When difficulties increased, my colleague Sunil K. Podder encouraged me with a quote by Madame Curie: "Life is not easy for any one of us. But what of that? We must have perseverance and above all, confidence in ourselves. We must believe that we are gifted for something ... and this thing, at whatever cost must be attained."

I am grateful to colleagues, staff and students in the department of biochemistry in the Indian Institute of Science for their courtesies and to the Department of Science & Technology, Government of India, for a book-writing grant.

Ramesh Maheshwari

Contents

PART I The Unique Features of Fungi

Chapter 1 The Hyphal Mode of Life 3

1.1 Features of Hyphae 3

1.1.1 Spread and Longevity 3

1.1.2 Indeterminate Growth 4

1.1.3 Apical Extension and Synchronized Growth 6

1.1.4 Spitzenkorper 6

1.1.5 Tip-High Calcium 8

1.1.6 Large Surface Area 9

1.1.7 Cytoskeleton 10

1.1.8 Protein Secretion 10

1.1.9 Nutrient Uptake 12

1.2 Cell Wall 13

1.2.1 Composition and Structure 13

1.2.2 Hydrophobins 14

1.3 Mycelium Formation 14

1.3.1 Septation 14

1.3.2 Branching 15

1.3.3 Hyphal Fusion 16

1.3.4 Multihyphal Structures 16

1.4 Concluding Remarks 17

References 17

Chapter 2 The Multinuclear Condition 19

2.1 Nuclear Number and Hyphal Growth 19

2.2 Chromosome Numbers 20

2.3 Nuclear Division Cycle 21

2.3.1 Temperature-Sensitive Mutants 22

2.3.2 Kinetics of Nuclear Division Cycle 23

2.4 Asynchronous Nuclear Divisions 23

2.5 Nuclear Migration 24

2.6 Positioning of Nuclei and Gene Regulation 25

2.7 Heterokaryosis 26

2.7.1 Sheltering of Lethal Mutation 27

2.7.2 Nuclear Selection 28

2.7.3 Nuclear Competence 29

2.8 Parasexual Recombination 30

2.9 Concluding Remarks 31

References 31

PART II Interactions of Fungi with Other Organisms

Chapter 3 Fungi as Symbiotic Partners 35

3.1 Mycorrhiza 35

3.1.1 Types of Mycorrhiza 36

3.1.2 Techniques of Studying Mycorrhizal Symbiosis 36

3.1.3 Diffusible Host and Fungal Factors 39

3.1.4 Differentially Expressed Plant Genes 40

3.1.5 Multiple Genomes 41

3.2 Lichen 42

3.2.1 Mycobiont and Photobiont 44

3.2.2 Lichen Synthesis 44

3.2.3 Transfer of Carbohydrate in Lichen Symbiosis 45

3.3 Some Unanswered Questions 45

References 45

Chapter 4 Fungi as Plant Pathogens 47

4.1 Early Ideas on Plant Diseases 47

4.2 Some Striking Fungal Diseases 49

4.2.1 Diseases of Crop Plants 49

4.2.2 Fungal Diseases of Trees 50

4.3 Classes of Plant Pathogenic Fungi 51

4.3.1 Necrotrophic and Biotrophic Fungi 51

4.4 General Features of Pathogenesis 51

4.4.1 Adhesion of Spores 53

4.4.2 Directional Growth 53

4.4.3 Infection Structures 54

4.4.4 Production of Cutinase 57

4.4.5 Production of Toxins 57

4.4.6 Detoxification of Saponins 58

4.5 Concluding Remarks 60

References 60

PART III Model Fungi in Research

Chapter 5 Neurospora: A Gateway to Biology 65

5.1 Habitat, Life Style and Life Cycle 65

5.2 Meiotic Events 70

5.3 Gene Maps 73

5.4 One Gene-One Enzyme Hypothesis 76

5.5 Molecular Revolution 78

5.6 Revelations from Genome Sequence 78

5.7 Concluding Remarks 79

References 80

Chapter 6 Yeast: A Unicellular Paradigm for Complex

Biological Processes 81

6.1 Introduction 81

6.2 Molecular Mechanisms of DNA Replication and Cell Division 82

6.2.1 cdc Genes 85

6.3 Bud Growth and Polarity 85

6.4 Mating and Signal Transduction Cascade 89

6.5 Protein Targeting 91

6.6 Mitochondrial Biogenesis 92

6.7 Functional Genomics 94

6.7.1 Number of Yeast Genes 96

6.7.2 Expression Pattern of Genes Using DNA Microarrays 98

6.7.3 Mapping Transcription Network 98

6.8 Proteomics and System Biology Modeling 100

6.9 Concluding Remarks 103

References 103

Chapter 7 Aspergillus nidulans: A Model for Study of Form and Asexual Reproduction 107

7.1 Conidiophore Morphogenesis 108

7.1.1 Developmental Competence 109

7.2 Microcycle Conidiation 109

7.3 Conidiation Genes 109

7.4 Conidiation Trigger 111

7.5 Regulatory Pathway 112

7.6 Summary 114

References 114

Chapter 8 Ustilago maydis: Mechanisms in Sexual

Reproduction 117

8.1 Heterothallism vs. Homothallism 117

8.2 Cell-Cell Recognition 118

8.2.1 Mating Types 118

8.3 Extracellular Recognition 121

8.3.1 The a Locus 121

8.3.2 Pheromone and Receptor 122

8.4 Intracellular Recognition 124

8.4.1 The b Locus 124

8.5 Overview 126

References 126

PART IV Gene Manipulation in Fungi

Chapter 9 Transformation of Fungi and Discovery of Gene-Silencing Phenomena 129

9.1 Transformation Procedure 129

9.2 Homologous vs. Ectopic Integration of Transgene 131

9.3 Purification of Transformant 132

9.4 Gene-Silencing Phenomena 132

9.4.1 Silencing by Mutation (RIP) 132

9.4.2 Meiotic Silencing by Unpaired DNA (MSUD) 134

9.4.3 Silencing by DNA Methylation (MIP) 135

9.4.4 Quelling 136

9.4.5 Internuclear Gene Silencing 140

9.5 Concluding Remarks 141

References 141

PART V Adaptations

Chapter 10 Thermophilic Fungi: Eukaryotic Life at High Temperature 145

10.1 Discovery 146

10.1.1 Self-Heating of Stored Agricultural Products 146

10.1.2 Guayule Rets 148

10.1.3 Composts 148

10.2 Distribution in Soil 148

10.3 Physiology 151

10.3.1 Cultivation 151

10.3.2 Metabolic Rate 152

10.3.3 Efficiency of Growth 153

10.3.4 Carbon Sources in Environment 153

10.3.5 Transport of Nutrients 153

10.3.6 Protein Turnover 154

10.4 Secretory Enzymes 154

10.4.1 Proteases 155

10.4.2 Lipases 155

10.4.3 Amylases 155

10.4.4 Cellulases 156

10.4.5 Xylanases 156

10.4.6 Cell-Associated Enzymes 156

10.5 Concluding Remarks 159

References 160

Chapter 11 Photoresponses and Circadian Rhythm 163

11.1 Types of Photoresponses in Fungi 163

11.1.1 Pigmentation 163

11.1.2 Growth Rhythms 163

11.1.3 Reproduction 164

11.1.4 Spore Liberation 165

11.1.5 Phototropism 166

11.1.6 Morphogenesis 169

11.2 Circadian Rhythm in Neurospora 170

11.2.1 A Clock Gene 171

11.2.2 Regulatory Genes 171

11.2.3 Clock-Controlled Genes 173

11.3 Entrainment 173

11.4 Summary 174

References 175

Chapter 12 Decomposition of Biomass 177

12.1 Decay of Wood and Litter 177

12.1.1 White-Rot and Brown-Rot Fungi 179

12.1.2 Litter Decomposers 179

12.2 Biochemistry of Degradation of Cell Wall Polymers 180

12.2.1 Lignin Degradation 180

12.2.2 Cellulose Degradation 182

12.2.3 Hemicellulose Degradation 187

12.3 Concluding Remarks 187

References 188

PART VI Populations

Chapter 13 Species, Their Diversity and Populations 191

13.1 Value of Diversity 191

13.1.1 Applied Research 191

13.1.2 Basic Research 193

13.2 Number of Fungal Species 194

13.3 Species Recognition 195

13.3.1 MSR, BSR and PSR 195

13.4 Discovery of Intraspecies Variability 196

13.4.1 Physiological Races 196

13.4.2 Vegetative Compatibility 197

13.5 Generation of Variation 197

13.5.1 Mutation and Heterokaryosis 197

13.5.2 Transposable Elements 198

13.6 Detection of Genetic Variation in Populations 198

13.6.1 Isozymes 198

13.6.2 RFLP 199

13.6.3 RAPD 199

13.6.4 Ribosomal DNA 201

13.6.5 Mitochondrial DNA and Mitochondrial Plasmids 202

13.6.6 DNA Sequence 202

13.6.7 Karyotype Polymorphism 203

13.6.8 Spore Killer Elements 203

13.7 Speciation 203

13.8 Concluding Remarks 204

References 205

Chapter 14 Senescence 207

14.1 Discovery of Senescing Strains 207

14.2 Distinguishing Nucleus and Mitochondria

Based Senescence 208

14.2.1 Genetic Cross 208

14.2.2 Heterokaryon Test 208

14.3 Senescence in Podospora anserina 209

14.3.1 Deletion and Rearrangements in Mitochondrial DNA 209

14.3.2 Nuclear Gene Control of Mitochondrial

DNA Deletions 212

14.4 Plasmid-Based Senescence in Neurospora 212

14.4.1 Mitochondrial Plasmids 212

14.5 Nuclear Gene Mutants 215

14.5.1 natural death 215

14.5.2 senescent 215

14.6 Aerobic Respiration, Aging and Senescence 218

14.7 Concluding Remarks 220

References 221

Appendix Naming, Defining, and Broadly Classifying Fungi 223

Naming of Fungi 223

Definition of a Fungus 223

Classification 224

A Broad Classification of Fungi 224

Kingdom Eumyccta 224

Phylum Chytridiomycotina 225

Phylum Zygomycotina 225

Phylum Glomeromycotina 225

Phylum Ascomycotina 228

Phylum Basidiomycotina 229

Phylum Deuteromycotina (Fungi Anamorphici) 229

Kingdom Straminipila (Stramenopila) 233

General References 233

Index 235

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