Fungal Genomics (eBook)

Fungal Genomics 4
Copyright Page 5
Contents 6
Contributors 10
Preface 14
Chapter 1: Genetics of Morphogenesis and Pathogenic Development of Ustilago maydis 15
I. Introduction 17
II. Mating 18
A. The mating loci 18
B. The a locus: Self/nonself-recognition 18
C. The b locus: Self/nonself-recognition 20
D. Targets of bE/bW regulation 21
E. The response to mating: Activation of cAMP and MAPK pathways 22
F. Interplay between the cAMP and MAPK pathways 24
III. Dimorphism 26
A. Low nitrogen 27
B. pH 28
C. Additional stimuli: Air and polyamines 29
D. Lipids as signals 29
E. Chitin synthases 30
IV. Cell Cycle and Cytoskeletal Regulation 31
A. Cell cycle 31
B. Microtubules and actin 32
C. Molecular motors and transport 33
D. Differences with other fungi 34
E. Connecting the signaling nodes 34
V. Pathogenesis 35
A. Penetration and colonization 35
B. Gall formation and in planta teliospore production 37
VI. Genome-Wide Approaches for the Study of U. maydis 41
A. Genome structure 41
B. An expanding toolbox for the study of U. maydis 44
C. Differential screens 45
D. Adapted for pathogenicity 48
VII. The Plant Side of the Disease Equation 50
VIII. Conclusion 52
References 52
Chapter 2: Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project 63
I. Introduction 65
A. Why study fungi? 66
B. Why Neurospora? 66
C. Overview of the functional genomics effort 69
II. Project 1: Systematic Gene Knockouts 70
A. Creation of gene knockouts in Neurospora 72
B. Basic phenotypic characterization of mutants 82
C. Deposition of the strains in the Fungal Genetics Stock Center (FGSC) and their distribution to the scientific community at large 83
D. Summary of gene knockouts 84
III. Project 2: Genome Informatics and Functional Annotation Studies 85
A. Introduction 85
B. Improving automated genome annotation 85
C. Community annotation 87
D. Annotation of allele-specific phenotypes 89
IV. Project 3: Profiling Transcription in Neurospora 92
A. Oligonucleotide design and synthesis 92
B. Experimental design for microarray experiments 93
C. Technical aspects to transcriptional profiling: RNA extraction, cDNA labeling, image acquisition, and normalization procedures 94
D. Neurospora functional genomics microarray database 95
E. Proof-of-principle: Transcriptional profiling of conidial germination 95
F. Future prospects 97
V. Project 4: cDNA Libraries and the Generation of a High-Density SNP Map 99
A. Introduction and rationale for the design of the project 99
B. Construction of the map 100
C. Validation of the SNP map 103
D. Implementation of the SNP map 106
VI. Conclusions 107
Acknowledgments 107
References 107
Chapter 3: Genomics of the Plant Pathogenic Oomycete Phytophthora: Insights into Biology and Evolution 111
I. Introduction 112
II. Advances in Structural Genomics 114
A. Current datasets 114
B. Expressed sequence tags 115
C. Genome sequencing 117
III. Organization of Phytophthora Genomes 118
A. Genetic maps 118
B. Gene distribution and structure 120
C. Overview of gene content 122
D. Noncoding and repetitive DNA 125
E. Transposable elements 126
IV. Other Genetic Elements 128
V. Tools for Functional Genomics 129
A. Transformation systems for Phytophthora 129
B. Heterologous systems for functional genomics 131
VI. Selected Areas of Phytophthora Research 132
A. Plant-Phytophthora interactions 132
B. Developmental biology 138
C. Transcription mechanisms 141
D. Evolution 144
VII. Conclusions and Prospects 145
Acknowledgments 146
References 146
Chapter 4: Sex and Virulence of Human Pathogenic Fungi 157
I. The Predominant Human Pathogenic Fungi 158
II. Sex in Fungal Pathogens: Cost Versus Benefit 160
III. Mating-Type Loci Are the Sex-Determining Regions in Fungi 162
IV. Sex in Cryptococcus 163
V. The Unusual Cryptococcus Mating-Type Locus 167
VI. Genome Sequencing Identified Mating-Type Locus in the "Asexual" C. albicans and Led to the Discovery of Mating 167
VII. Mating-Type Locus in A. fumigatus 171
VIII. Mating-Type Loci in Other Human Pathogenic Fungi 171
IX. Population Genetic Studies in "Asexual" Fungi Reveal Evidence of Sex 173
X. The Role of Sex in Pathogenesis 176
XI. Concluding Remarks 179
References 180
Chapter 5: From Genes to Genomes: A New Paradigm for Studying Fungal Pathogenesis in Magnaporthe oryzae 189
I. Introduction 190
II. Attachment and Appressorium Morphogenesis 191
A. Attachment and germination 191
B. Surface recognition and cAMP signaling 192
C. Appressorium formation and maturation 196
D. The Pmk1 MAP kinase pathway 198
E. Genes expressed during appressorium formation 201
III. Mechanisms of Penetration 201
A. Penetration peg formation and penetration forces 201
B. Appressorium turgor generation 202
C. Appressorial penetration involves many coordinated processes 203
IV. Invasive Growth and Host-Pathogen Interactions 204
A. Infectious hyphal growth 204
B. Genes involved in race-specific interactions 205
C. Physiological activities of infectious hyphae 206
D. Genes involved in infectious growth 208
V. Genes and Genome Features 209
A. Genome sequence and annotation 209
B. Gene families and secreted proteins 210
C. Chromosome organization 211
D. Colinearity 212
E. Repetitive sequences 213
F. Receptors 214
G. Secondary metabolism and phytotoxic compounds 214
H. Repeat-induced mutation and silencing 216
VI. Functional Genomics 218
A. Large-scale mutagenesis 218
B. Genome-wide transcriptional profiling 220
VII. Concluding Remarks 222
Acknowledgments 223
References 223
Chapter 6: Genetic and Genomic Dissection of the Cochliobolus heterostrophus Tox1 Locus Controlling Biosynthesis of the Polyketide Virulence factor T-toxin 233
I. Introduction 234
A. C. heterostrophus biology 235
B. Cochliobolus and disease 237
II. Tools for Genetic Analysis 242
A. Classical genetics 242
B. Molecular genetics 242
C. Electrophoretic karyotype analysis 246
D. Restriction fragment length polymorphism mapping 246
III. C. heterostrophus and SCLB 247
A. T-toxin 247
B. T-cytoplasm corn and URF13 protein 247
C. Microbial bioassay for T-toxin production 249
IV. The Genetics of T-Toxin Production 249
A. The Tox1 locus 249
B. Identification of genes at Tox1 254
V. Genomic Analysis of the Tox1 Locus 256
A. cDNA profiling 256
B. Tox1-associated genome scaffolds 257
VI. The PM-Toxin Gene Cluster 261
VII. Are Additional Tox Loci Involved in T-Toxin Production? 263
VIII. Model for Biosynthesis of T-Toxin 264
IX. The Evolution of Polyketide-Mediated Fungal Specificity for T-Cytoplasm Corn 266
X. Conclusions 268
Acknowledgments 269
References 269
Chapter 7: Fungal Genomics: A Tool to Explore Central Metabolism of Aspergillus fumigatus and Its Role in Virulence 277
I. Introduction 278
II. Nutritional Auxotrophy and Fungal Genetics 279
III. Regulation of Amino Acid Biosynthesis 282
IV. Regulation of Ambient pH Response 286
V. Regulation of Nitrogen Response Pathways 289
VI. Regulation of Carbon Response Pathways 291
VII. Concluding Remarks 295
References 295
Index 299