International Review of Cell and Molecular Biology (eBook)

Front Cover 1
International Review of Cell and Molecular Biology 2
International Review of Cell and Molecular Biology 3
International Review of Cell and Molecular BiologyEdited byKWANG W. JEONDepartment of Biochemistry University of TennesseeK ... 4
Copyright 
5 
Contents 6
Contributors 10
How Rab Proteins Determine Golgi Structure 14
1. Introduction 15
2. Rab Proteins and Their Subfamilies 16
3. Golgi Apparatus and Its Organization 18
4. Two Major Functional/Phenotypic Classes of Rab Proteins Based on Their Effects on Golgi Ribbon Organization 20
5. Mechanistic Effect of Rab Proteins on Golgi Ribbon Organization 26
5.1 General Mechanistic Predictions 26
5.2 Rab6 and the Role of Individual Effectors 26
5.3 Role of Rab33b in Rab6-Dependent Golgi Ribbon Organization 29
5.4 Opposing Effects of Rab41 and Rab6 on Golgi Ribbon Organization 29
6. Conclusions and Perspectives 30
Acknowledgments 31
References 31
Amyotrophic Lateral Sclerosis as a Spatiotemporal Mislocalization Disease: Location, Location, Location 36
1. Introduction 37
2. Amyotrophic Lateral Sclerosis 38
2.1 Models for ALS Research 39
3. Axonal Transport 41
3.1 Axonal Cytoskeleton 41
3.2 Motor Proteins 44
3.3 Mitochondrial Transport 47
4. RNA-Binding Proteins 51
4.1 Tar DNA-Binding Protein 43 51
4.2 Fused in Sarcoma 53
4.3 MicroRNA and RBP 53
4.4 Chromosome 9 Open Reading Frame 72 55
5. Neurotrophic Factors and Their Precursor Forms 56
6. Death Signals 59
6.1 p75 Neurotrophin Receptor 61
6.2 Death Receptor 6 62
6.3 Fas 62
6.4 Semaphorins 63
7. Amyloid Precursor Protein 64
8. Concluding Remarks 65
Acknowledgments 68
References 68
Malleable Mitochondrion of Trypanosoma brucei 86
1. Introduction 87
2. Maintenance and Expression of Genetic Information 89
2.1 kDNA Replication and Maintenance 90
2.2 Mitochondrial RNA Metabolism 94
2.2.1 Transcription 94
2.2.2 RNA processing 94
2.2.3 RNA editing 97
2.2.4 RNA turnover 100
2.2.5 Mitochondrial tRNA import and modifications 101
2.3 Translation and Ribosomes 105
3. Mitochondrial Import 107
3.1 Protein Import and Processing 107
3.2 Transport of Metabolites 113
3.3 Transport of Ions 115
4. Mitochondrial Metabolism 117
4.1 Carbohydrate Metabolism—Krebs Cycle 118
4.2 Oxidative Phosphorylation 122
4.3 Fatty Acid Biosynthesis 126
4.4 Metabolism of Amino Acids 128
4.5 Metabolism of Cofactors 131
4.5.1 Heme metabolism 131
4.5.2 Fe-S cluster and protein biogenesis 132
5. Structural Proteins and Fission 137
6. Concluding Remarks 139
Acknowledgments 140
References 140
Heredity and Self-Organization: Partners in the Generation and Evolution of Phenotypes 166
1. Introduction 167
2. Self-Organization in Biology 169
2.1 Genes versus Cell Numbers 169
2.2 Molecular Self-Organization and DNA 169
2.3 Mechanical Forces and Self-Organization 170
2.4 Self-Organization of Complex Biological Structures 171
2.5 Dynamics 171
2.6 Functional Plasticity May Be Based on Self-Organized Processes at Different Biological Scales 173
2.7 Dynamics: Self-Organized Component of Developmental Robustness 177
3. Internal Descriptions, Developmental Limitations and Buffering Variation 182
3.1 What Constitutes the Internal Description of Biological Organisms? 182
3.2 “Internal Descriptions” and the Concept of a Genotype–Phenotype Map 183
3.3 Self-Organization and Evolutionary Variation 184
3.3.1 Developmental Improbabilities and Drosophila Sex Comb Length 185
3.3.2 Self-organization and Pleiotropy 186
3.3.3 Reduction in Variation in D. melanogaster Sex Comb Alignment 189
4. Conclusions 190
Acknowledgments 191
References 191
Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication 196
1. Introduction 197
2. Juxtaposition of Genome Regulatory Elements: Active Chromatin Hub or Active Nuclear Compartment? 199
3. Dynamic Contacts rather than Rigid Complexes 203
4. Driving Forces of Communication within Cell Nucleus 207
4.1 Long-Range Interactions and TADs: Communication for Folding or Folding for Communication? 207
4.2 Communication Mediated by Molecular Motors: RNAPolII and Nuclear actin/Myosin I System 212
4.3 Free Diffusion and Macromolecular Crowding 217
5. Functional Compartmentalization of Eukaryotic Cell Nucleus 219
5.1 Spatial Organization of Eukaryotic Genome: View under Microscope 220
5.2 Functional Nuclear Compartments 223
5.2.1 Nuclear compartments (nuclear bodies) that contain DNA 223
5.2.1.1 Replication factories 223
5.2.1.2 Transcription factories 224
5.2.1.3 Polycomb bodies 226
5.2.1.4 Insulator bodies 227
5.2.2 Nuclear compartments (nuclear bodies) that do not contain DNA 227
5.2.2.1 PML bodies 228
5.2.2.2 Cajal bodies and histone locus bodies 229
5.2.2.3 Nuclear speckles 230
6. Nuclear Compartmentalization and Chromosome Folding: Attempt to Present Integral View 231
7. Concluding Remarks 237
Acknowledgments 239
References 239
Modifiers of Membrane Dipole Potentials as Tools for Investigating Ion Channel Formation and Functioning 258
1. Introduction 259
2. Lipid Bilayers and Methods Used for Studying Effects of Dipole-Modifying Agents on Membrane Conductance 263
2.1 Electrical Model of Lipid Bilayers 263
2.2 Measurements of Dipole Potential 265
3. Factors Affecting Magnitude of Membrane Dipole Potential 267
3.1 Membrane Lipid Composition 267
3.2 Adsorption of Dipole-Modifying Agents 269
3.2.1 Flavonoids 269
3.2.2 Styryl dyes 271
3.2.3 Xanthene dyes 272
3.2.4 N-acylhomoserine lactones 272
3.2.5 Thyroid hormones 273
3.2.6 Other bioactive compounds 274
3.3 Microdomains Present within Membranes: Raft-Breaking and Raft-Making Effects of Dipole Modifiers 275
4. Effect of Dipole Potential on Channel-Forming Activity of Antimicrobial Agents 276
4.1 Lipopeptides 276
4.1.1 Syringomycin E 277
4.1.2 Surfactin 278
4.2 Peptides 280
4.2.1 Gramicidin A 281
4.2.2 Alamethicin 282
4.2.3 Cecropins 283
4.3 Polyene Macrolides: Amphotericin B 284
5. Effects Resulting from Modulation of Other Physical Properties of Lipid Bilayers by Dipole-Modifying Agents 285
5.1 Phase Separation in Lipid Bilayers 285
5.1.1 Amphotericin B and phase segregation in lipid membranes 286
5.1.2 Syringomycin E in sphingolipid-containing membranes 287
5.2 Spontaneous Curvature of Monolayers 289
5.2.1 Melittin 290
5.2.2 Magainin 291
5.2.3 Alamethicin 292
5.2.4 Gramicidin A 292
6. Interaction between Dipole Modifiers and Channel-Forming Molecules 295
6.1 Voltage Gating of Single Alpha-Hemolysin Pore 295
6.2 Amphotericin B-sterol complexes 296
7. Concluding Remarks 299
Acknowledgments 299
References 299
Link between Aneuploidy and Chromosome Instability 312
1. Introduction 312
2. Effect of Aneuploidy on Cellular Homeostasis 313
2.1 Transcriptome 314
2.2 Proteome 316
3. Effect of Aneuploidy on Chromosome Stability 317
3.1 DNA Replication and Condensation 319
3.2 Chromosome Segregation 320
4. Role of Aneuploidy and CIN in Adaptation and Disease 321
4.1 Unicellular Organisms 322
4.2 Multicellular Organisms 323
5. Conclusions and Perspectives 324
Acknowledgments 325
References 326
INDEX 332