Biochemistry and Molecular Biology (eBook)

Professor Dr. Dirk Hoffmeister Friedrich-Schiller-Universität, Pharmazeutische Mikrobiologie, Jena, Germany

Series Preface 8
Volume Preface 12
Contents 14
List of Contributors 16
Regulation of Gene Expression 20
1 Molecular Biology of Asexual Sporulation in Filamentous Fungi 21
I. Introduction 21
II. Asexual Sporulation in Aspergillus nidulans 21
A. Morphology of Asexual Structure 21
B. Regulators of Asexual Development 22
1. Central Regulators of Conidiation 22
a) BrlA 22
b) AbaA 23
c) WetA 23
d) StuA and MedA 23
2. Controllers of the Central Regulators 24
a) FluG-Mediated Signaling Pathway 24
b) Heterotrimeric G Protein Signaling Pathways 25
c) MAP Kinase Signaling Pathways 26
d) The Velvet Family Proteins 26
e) Light and Signals 27
f) Developmental Balancers 27
g) Other Transcription Factors 28
3. Feedback Regulators of Conidiation 28
III. Asexual Sporulation in Penicillum marneffei 28
A. Morphology of Asexual Structure 28
B. Regulators of Asexual Development 30
IV. Asexual Sporulation in Fusarium graminearum 30
A. Morphology of Asexual Structure 30
B. Regulators of Asexual Development 31
V. Conclusions 32
References 33
2 Insight into Fungal Secondary Metabolism from Ten Years of LaeA Research 38
I. Introduction 38
II. LaeA Mechanism 39
A. Methyltransferase 39
B. Epigenetics 39
C. Velvet Complex Member 39
III. Secondary Metabolites Regulated by LaeA 40
A. Aspergillus species 40
B. Other Genera 40
IV. Processes Identified Through LaeA Microarrays 42
V. Processes Identified Through LaeA Mutagenesis 42
VI. Conclusion 43
References 43
3 RNAi Function and Diversity in Fungi 47
I. Introduction 47
A. Evolution of RNAi and Its Protein Components 48
II. RNAi Function 49
A. Quelling 50
B. Meiotic Silencing by Unpaired DNA 52
C. Heterochromatin Formation and Transcriptional Gene Silencing 53
D. Sex-Induced Silencing 55
III. MicroRNAs 55
IV. RNAi During Plant-Microbe Interaction 56
V. RNAi as a Biotechnology Tool 57
VI. Conclusion 58
References 58
4 Fungal Molecular Response to Heavy Metal Stress 62
I. Introduction 63
II. Thou Shall Not Pass!: Extracellular Response upon Metal Toxicity 65
A. Metal Sorption to the Cell Wall 65
B. Release of Metal-Binding Substances 67
1. Interaction of Organic Acids with Metals 67
2. Oxalic Acid 68
3. Further Organic Acids 68
4. Siderophores 69
5. Glutathione 69
III. Leave Someone Holding the Baby: Intracellular Processes and Transport 69
A. Regulation of Metal Influx 69
B. Metal Efflux Systems 71
C. Chelation and Chelate Transport 72
IV. System Reset: Alleviating Metal-Induced Damage 73
V. Perspective 74
References 75
5 Control of Gene Expression in Phytopathogenic Ascomycetes During Early Invasion of Plant Tissue 84
I. Introduction 84
A. Fungal Lifestyles 84
B. Comparative Genomics 84
C. Stages of Infection 85
II. Surface Recognition and Breaking Dormancy 88
A. Surface Recognition 88
B. Adhesion 89
C. Germination 91
III. Entry into the Plant 92
A. Direct Entry 93
1. Infection Structure-Initiated Entry 93
a) Developing Appressoria in Magnaporthe oryzae 93
b) Gene and Protein Expression in Mature Appressoria 94
i. Magnaporthe oryzae 94
ii. Colletotrichum Species 94
iii. Blumeria graminis 95
iv. Botrytis cinerea 96
v. Sclerotinia sclerotiorum 96
vi. Parastagonospora nodorum 97
B. Entry Through Stomata or Wounds 98
1. Gene Expression During Early Infection 99
a) Zymoseptoria tritici 99
b) Fusarium graminearum 100
c) Leptosphaeria maculans 100
d) Cladosporium fulvum 101
IV. Conclusions 102
References 102
Signal Transduction 110
6 Fungal MAP-Kinase-Mediated Regulatory Pathways 111
I. Introduction 111
II. The Pheromone Response and Filamentation MAPK Pathways 112
A. Saccharomyces cerevisiae 112
1. Pheromone Response in S. cerevisiae 112
2. Filamentous Growth of S. cerevisiae 114
B. Candida albicans 115
C. Filamentous Fungi 115
1. Aspergillus nidulans and Aspergillus fumigatus 115
2. Neurospora crassa 118
3. Cryptococcus neoformans 118
4. Plant Pathogenic Fungi 119
III. The Stress Response MAPK Pathway 119
A. Saccharomyces cerevisiae 120
B. Candida albicans 120
C. Filamentous Fungi 121
1. Aspergillus nidulans and Aspergillus fumigatus 121
2. Neurospora crassa 121
3. Cryptococcus neoformans 121
4. Plant Pathogenic Fungi 122
IV. The Cell Wall Integrity (CWI) Pathway 122
A. Saccharomyces cerevisiae 122
B. Candida albicans 123
C. Filamentous Fungi 123
1. Aspergillus nidulans and Aspergillus fumigatus 123
2. Neurospora crassa 124
3. Cryptococcus neoformans 124
4. Plant Pathogenic Fungi 124
V. Spore Morphogenesis in Saccharomyces cerevisiae 125
VI. Conclusions 125
References 126
7 Heterotrimeric G Proteins 132
I. Introduction 132
II. Components of Heterotrimeric G Protein Signaling 133
A. G?, Gbeta, and Ggamma Proteins 133
B. Guanine Nucleotide Exchange Factors (GEFs) 136
1. G Protein-Coupled Receptors (GPCRs) 136
2. Non-receptor GEFs 136
C. Regulator of G Protein Signaling (RGS) Proteins 138
D. Effector Pathways 138
1. cAMP-Dependent Protein Kinase (PKA) 138
2. Mitogen-Activated Protein Kinase (MAPK) 139
IV. Cellular Functions of G Protein Signaling Components in Yeast and Filamentous Fungi 140
A. Nutrient Sensing 140
1. Glucose Sensing in Saccharomyces cerevisiae and Schizoaccharomyces pombe 140
2. Carbon-Sensing Pathways in Neurospora crassa and Aspergillus nidulans 141
3. Methionine and Glucose Sensing in Cryptococcus neoformans 141
B. Mating and Pheromone Response 142
1. Ste2p/?-Factor and Ste3p/a-Factor in S. cerevisiae 142
2. Map3/M-Factor and Mam2/P-Factor in S. pombe 142
3. PRE-1/MFA-2 and PRE-2/CCG-4 in N. crassa 143
4. Mating and Cleistothecia Formation in Aspergillus 143
5. Mating in Cryptococcus neoformans 144
C. Pathogenesis and Virulence 144
1. Appressorium Formation and Pathogenicity in Magnaporthe oryzae 144
2. Pathogenesis in Ustilago maydis 146
3. Melanin and Capsule Formation in Cryptococcus neoformans 147
4. Quorum Sensing in Aspergillus 147
IV. Conclusions 148
References 148
Molecular Biology and Biochemistry of Fungal Carbohydrates 158
8 The Cell Wall Polysaccharides of Aspergillus fumigatus 159
I. Introduction 159
II. The Cell Wall of Aspergillus fumigatus Hyphae 160
III. Synthesis and Function of Cell Wall Polysaccharides 161
A. beta-1,3-glucan 161
B. Chitin 163
C. Galactomannan 163
D. ?-1,3-glucan 164
E. Galactosaminogalactan 165
IV. Modifications of Cell Wall Polysaccharides 165
A. Modification of beta-1,3-glucans 165
1. Endo-beta-1,3-glucanase (ENG Proteins) 166
2. beta-glucanosyltransferase (GEL Proteins) 166
3. Branching Enzymes, BGT Proteins 166
4. Other beta-1,3-glucan-Modifying Enzymes (EXO and SUN Proteins) 167
B. Modification of Chitin 167
1. Chitinase, CHI Proteins 167
2. Chitin Deacetylase, CDA Proteins 167
3. Chitosanase, CSN Proteins 168
C. Modification of Other Cell Wall Polysaccharides 168
V. Towards an Understanding of the Regulation of Cell Wall Biosynthesis 169
A. Chemogenetic Approaches to Understanding the Regulation of Cell Wall Biosynthesis 169
B. Deciphering the Regulation of Cell Wall Composition Through Direct Molecular Approaches 170
1. Global Regulators of Cell Wall Biosynthesis 170
2. Other Compensatory Relationships Between Cell Wall Polysaccharides 171
C. Real World Applications: Targeting Compensatory Changes in Cell Wall Composition to Enhance Antifungal Efficacy 172
VI. Conclusions and Perspectives 172
References 172
9 Chitin Synthesis and Fungal Cell Morphogenesis 178
I. Introduction 178
II. Chitin Synthases and Deposition of Chitin at the Fungal Cell Wall 179
III. Chitin Synthases 180
A. The Diversity of Fungal Chitin Synthases: A Common Catalytic Centre for Multiple Functions 180
B. The Ancient Evolutionary Origin of Chitin Synthases 182
IV. Chitin Synthesis and Fungal Cell Wall Assembly 183
A. Chitin Synthesis and Cell Wall Assembly 183
B. Chitin Degradation and Cell Wall Assembly 185
C. Chitin Synthesis in Response to Cell Stress 185
V. A Single Polymer but Distinct Functions for Chitin Synthase Enzymes 185
A. The Biological Function of Family I CSs 185
1. Chitin Synthase I 186
2. Chitin Synthase II 186
3. Other Class I, II and III Fungal CSs 186
B. The Biological Function of Family II CSs 187
1. Chitin Synthase III (Class IV) 187
2. Chitin Synthases with Myosin Motor-Like Domain 187
C. The Elusive Function of Class VI CSs 188
VI. Regulation of Chitin Synthases 188
A. Regulation of Family I CSs 189
1. Regulation of Chitin Synthase I 189
2. Regulation of Chitin Synthase II 189
3. Regulation of Other Class I, II and III Fungal CSs 191
B. Regulation of Family II CSs 192
1. Regulation of Chitin Synthase III 192
2. Regulation of Fungal Chitin Synthases During Mycelial Growth: Chitin Synthases with a Myosin Motor-Like Domain 194
VII. Chitin Synthesis and Antifungal Therapies 195
VIII. Concluding Remarks 196
References 196
10 Trehalose Metabolism: Enzymatic Pathways and Physiological Functions 202
I. Introduction 203
II. Occurrence of Trehalose 204
III. Biosynthetic Pathways for Trehalose 206
A. Trehalose-6-Phosphate Synthase and Phosphatase 207
B. Trehalose Phosphorylase 211
IV. Enzymes of Trehalose Hydrolysis: Trehalases 212
V. Functions of Trehalose 215
A. Trehalose as Storage Carbohydrate 215
B. Trehalose as Stress Protectant 217
1. Trehalose as Stress Protectant In Vitro 217
2. Trehalose as Stress Protectant In Vivo 218
3. Trehalose and Thermotolerance 220
4. Trehalose and Freeze Tolerance 221
5. Trehalose and Osmo- and Dehydration Tolerance 222
6. Trehalose and Other Stress Conditions 223
7. Other Stress Protectants 225
C. Trehalose as Carbon Source 226
1. Transport of Trehalose 226
D. Other Functions of Trehalose 228
VI. Regulation of Trehalose Metabolism 229
A. Cellular Signaling Pathways Controlling Trehalose Metabolism 229
1. Glucose-Induced Trehalose Mobilization: cAMP as Second Messenger 229
2. Fermentable-Growth-Medium-Induced Trehalose Mobilization: Nutrient Sensing by Transceptors 232
a) Nitrogen-Induced Trehalose Mobilization 233
b) Phosphate-Induced Trehalose Mobilization 234
c) Sulfate-Induced Trehalose Mobilization 235
d) Induction of Trehalose Mobilization by Other Nutrients 235
B. Posttranslational and Transcriptional Control of Trehalose Biosynthesis and Degradation 236
1. Posttranslational Regulation of Trehalose Biosynthesis 236
2. Posttranslational Regulation of Trehalose Degradation 238
3. Transcriptional Regulation of Trehalose Biosynthesis and Degradation 240
4. Trehalose Accumulation During Sublethal Heat Treatment 242
VII. Regulatory Functions of Trehalose Metabolism 246
A. Control of Growth, Cell Cycle Progression, and Sporulation 246
B. Control of Glycolysis by Tre6P 248
C. Yeast as a Model for Plant Trehalose Metabolism 254
VIII. Trehalose Metabolism as a Target for Antifungal Compounds 255
IX. Conclusions and Perspectives 260
References 260
Molecular Aspects of Biochemical Pathways 289
11 Regulation of Fungal Nitrogen Metabolism 290
I. Introduction 290
II. Regulation by Global and Pathway-Specific Transcription Factors 291
III. Global Regulation of Nitrogen Utilization Genes 292
A. Transcriptional Controls: The Key Players 292
1. The GATA Transcription Factor AreA 292
a) AreA Function 292
b) Conservation of AreA Function 293
c) Regulation of AreA Action 294
d) Regulation of areA mRNA Stability via Caf1, CutA, and RrmA 294
e) Regulation of AreA Subcellular Localization 294
f) Nitrogen Regulation via TOR Signaling 297
g) Unconventional Modes of AreA Action 297
2. The Corepressor NmrA 298
a) NmrA Function 298
b) Conservation of NmrA 299
c) Regulation of NmrA Function 299
3. The bZIP Transcription Factor MeaB 300
a) MeaB as a DNA-Binding Protein 300
b) Conservation of MeaB 301
c) Regulation of MeaB 301
4. AreB: A Second GATA Transcription Factor 302
a) AreB Is a Transcription Repressor of Nitrogen Metabolic Genes 302
b) Conservation of AreB 303
5. The Dual-Function Transcription Factor TamA 304
a) TamA Is a Coactivator of AreA 304
b) TamA Acts as a DNA-Binding Activator or as a Coactivator Depending on Promoter Context 304
c) Conservation of TamA 306
B. Posttranscriptional Controls 306
IV. Conclusions 306
References 307
12 Regulation of Sulfur Metabolism in Filamentous Fungi 313
I. Introduction 313
II. Acquisition of Sulfur 314
A. Sulfur Sources 314
B. Response to Sulfur Limitation 315
III. Detection of Sulfur Status 317
IV. Neurospora crassa Sulfur Regulatory System 319
A. CYS3 Regulator 319
B. Sulfur Controller Regulators 321
C. Operation of the Control System 322
V. Regulatory Comparison to Aspergillus nidulans and Saccharomyces cerevisiae 323
VI. Conclusions 324
References 325
13 The Regulation of Carbon Metabolism in Filamentous Fungi 328
I. Introduction 328
II. Glucose Transport and Sensing 329
III. Induction and Repression 330
IV. Carbon Catabolite Repression 331
A. CreA 331
1. A. nidulans creA Mutations 331
2. CreA Mutant Phenotypes in Other Fungi 332
3. Molecular Analysis of CreA in A. nidulans 332
4. Functional Analysis of CreA 334
5. Comparison Between Yeast and A. nidulans, and Within Filamentous Fungi 334
B. A Role for Regulatory Ubiquitination 337
1. A Role for Deubiquitination? 337
2. A Role for Ubiquitination? 339
V. Genome-Wide Studies 340
VI. Concluding Remarks 341
References 342
14 Special Aspects of Fungal Catabolic and Anabolic Pathways 348
I. Introduction 348
II. Propionyl-CoA, A Common Metabolic Intermediate 349
A. Degradation of Propionyl-CoA via the Methylcitrate Cycle 351
B. Alternative Propionyl-CoA Degradation Pathways in Fungi 352
III. Growth on Gluconeogenic Substrates 355
A. Utilisation of the Glyoxylate Cycle in Ascomycetes 355
IV. Amino Acid Biosynthesis and Utilisation as Nutrient Sources 357
A. Histidine Degradation in Fungi 358
B. Synthesis of the Amino Acid Lysine 360
V. Conclusions 363
References 363
15 Genetic and Metabolic Aspects of Primary and Secondary Metabolism of the Zygomycetes 368
I. Introduction 368
A. Zygomycetes: Evolution, Systematics, and Ecology 369
B. The Cooperative Nature of Zygomycetes: Bacterial-Fungal Alliances 370
II. Key Aspects in the Metabolism of Zygomycetes: Biotechnological Implications 371
A. Carotene Biosynthesis and Degradation: Primary Meets Secondary Metabolism 372
1. Regulation, Genetic Manipulation: What Have We Learned from the Major Model Organisms Mucor circinelloides, Phycomyces blak... 374
2. Carotene Degradation Is Linked to Sexual Interactions 377
B. Fatty Acids 379
C. Organic Acids 379
D. Storage Lipids and Single Cell Oils 380
E. Enzymes 381
III. The Dogma of the Unability of Zygomycetes to Produce Natural Products 382
IV. Conclusions 384
References 384
Biosystematic Index 393
Subject Index 397