Plant Mitochondria (eBook)

Frank Kempken graduated from the Ruhr-University Bochum, Germany. He is professor for genetics and molecular biology in botany at the Christian-Albrechts-University at Kiel, Germany.

Preface 8
Contents 12
Part I: 
Genomes 15
Chapter 1: Mitochondrial Genome Evolution in the Plant Lineage 16
1.1 Introduction 16
1.2 Land Plant Mitochondrial DNAs and Their Peculiarities 17
1.3 Plant Mitochondrial Genomes: Completed MtDNA Sequences 20
1.4 Ongoing Gene Transfer to the Nucleus 21
1.5 Plant Mitochondrial Genomes: Structures 24
1.6 The Introns in Embryophyte Mitochondrial DNAs 25
1.7 RNA Editing 27
1.8 Gene Transfer Deviations: Promiscuous DNA 29
1.9 Horizontal Gene Transfer 30
1.10 An Extended Perspective: What Else? 31
References 33
Chapter 2: Mitochondrial Dynamics 43
2.1 Introduction 43
2.2 Division 45
2.2.1 Animal and Yeast Mitochondrial Division 45
2.2.2 Plant Mitochondrial Division 53
2.3 Fusion 55
2.3.1 Animal and Yeast Mitochondrial Fusion 55
2.3.2 Plant Mitochondrial Fusion 56
2.4 Regulation of Chondriome Structure 57
2.4.1 Temporal Regulation 57
2.4.2 Physical Regulation 58
2.5 Death 59
2.6 Motility, Distribution, and Inheritance 61
2.6.1 Mitochondrial Movement and the Cytoskeleton 61
2.6.1.1 Mitochondrial Movement and Microtubules 62
2.6.1.2 Mitochondrial Movement and Actin 63
Myosin 63
Mechanisms Other Than Myosin-Based 63
2.6.2 Mitochondrial Motility Delivers the Organelle to the Right Places 64
2.6.3 Inheritance and Cellular Distribution 65
2.7 Conclusions 66
References 67
Chapter 3: Plant Mitochondrial Genomes and Recombination 76
3.1 Why Study Plant Mitochondrial Genomes? 77
3.2 The Importance of Double Strand Breaks in Plant Mitochondria 77
3.3 Plant Mitochondrial Recombination Is Under Nuclear Gene Control 79
3.4 The Genetic Variability of Plant Mitochondria 82
3.4.1 Large (> 1,000-bp) Repeated Sequences
3.4.2 Intermediate (ca. 50 to 500-bp) Repeated Sequences 84
3.4.3 Small (4–25 bp) Repeated Sequences 85
3.5 Other Interpretations of Mitochondrial Genetic Variation 86
3.6 Mitochondrial Recombination Influences Plant Development 87
3.7 Could Mitochondrial Status, Conditioned by Recombination, Influence Plant Adaptation? 88
References 89
Part II: 
RNA Processing 94
Chapter 4: Transcription in Plant Mitochondria 95
4.1 Introduction to Mitochondrial RNA Polymerases 95
4.1.1 Evolution 95
4.1.2 Plant Mitochondrial RNA Polymerases 97
4.2 Plant Mitochondrial Promoters 100
4.3 Trans-Acting Factors Involved in Plant Mitochondrial Transcription 103
4.3.1 General Transcription Factor(s) 103
4.3.2 Specific Transcription Factors 105
4.4 Transcriptional Regulation of Mitochondrial Gene Expression 106
References 109
Chapter 5: RNA Processing and RNA Stability in Plant Mitochondria 116
5.1 Introduction 117
5.2 The Mitochondrial Transcriptome in Arabidopsis thaliana 117
5.3 Formation of Mature Mitochondrial mRNAs in Higher Plants 120
5.4 5' End Processing of Mitochondrial mRNAs 
121 
5.5 Posttranscriptional Generation of 3' Ends 
126 
5.6 mRNA Stability 129
5.7 CMS, Posttranscriptional Processes, and PPR Proteins 131
5.8 Mitochondrial tRNA Processing 131
5.9 Generation of Mature rRNAs in Plant Mitochondria 133
5.10 Conclusions 134
References 136
Chapter 6: RNA Splicing in Plant Mitochondria 140
6.1 Introduction 140
6.2 Distribution of Introns in Mitochondrial Genes of Land Plants 143
6.3 Trans-Splicing Introns 148
6.4 Mechanism of Splicing in Plant Mitochondria 149
6.5 Splicing Machinery for Plant Mitochondrial Introns 153
6.6 Relationship Between Splicing and Other RNA Processing Events in Plant Mitochondria 157
6.7 Concluding Remarks 158
References 159
Chapter 7: RNA Editing in Higher Plant Mitochondria 165
7.1 Introduction 165
7.2 Extent and Consequences of RNA Editing in Higher Plant Mitochondria 166
7.2.1 Extent of RNA Editing 166
7.2.2 Consequences of RNA Editing 168
7.3 Functional Analysis of the Higher Plant RNA Editing Mechanism 170
7.3.1 The Use of In vitro and In Organello Systems 170
7.3.2 What Can Be Learned from Plastid RNA Editing? 172
7.3.3 Mitochondrial RNA Editing Factors 173
7.4 Evolution of RNA Editing 175
7.5 Concluding Remarks 177
References 178
Chapter 8: RNA-Binding Proteins Required for Chloroplast RNA Processing 184
8.1 Introduction 184
8.2 The Pentatricopeptide Repeat Proteins 185
8.2.1 Structure 188
8.2.2 Evolution 190
8.2.3 Functions of PPR Proteins 191
8.2.4 RNA Recognition by PPR Proteins 193
8.3 The Plant Organellar RNA Recognition (PORR) Family 194
8.4 Chloroplast Ribonucleoproteins 194
8.4.1 Structure, Evolution, and RNA Targets 194
8.4.2 Expression 195
8.4.3 Functions 195
8.5 Whirly Proteins 196
8.6 Chloroplast RNA Splicing and Ribosome Maturation (CRM) Proteins and Associated Factors 197
8.6.1 Evolution and Structure of the CRM Proteins 197
8.6.2 Plant CRM Proteins Are Polyvalent Splicing Factors 198
8.6.3 CRM Ribonucleoprotein Particles 198
8.6.4 CRM-Associated Factors 199
8.6.5 CRS1: Highlighting the Molecular Mechanism Behind CRM Domain Functions 200
8.7 Orphan Chloroplast RNA-Binding Proteins 200
8.8 Outlook 201
References 205
Part III: 
Import 211
Chapter 9: The Plant Mitochondrial Proteome Composition and Stress Response: Conservation and Divergence Between Monocots and Dicots 
212 
9.1 Introduction 214
9.2 Overall Comparisons of Monocot and Dicot Mitochondrial Proteomes 218
9.3 Specific Examples of Conservation of Plant Mitochondrial Proteome and Function Between Monocots and Dicots 219
9.4 Specific Examples of Divergence in Plant Mitochondrial Proteome Monocots and Dicots 220
9.5 Plant Mitochondrial Proteome Responses to Abiotic Stress 222
9.6 Future Directions 237
9.6.1 Excluding Contaminants by Quantitative Analysis 237
9.6.2 In-depth Identification of Mitochondrial Proteins 238
9.6.3 Refining Quantitative Analysis of Proteome Differences of Biologic Consequence 239
9.6.4 Database Development and Access 240
References 241
Chapter 10: Import of RNAs into Plant Mitochondria 245
10.1 Introduction 246
10.2 What Are the Imported tRNAs in Photosynthetic Organisms? 246
10.2.1 The Number and Identity of Mitochondrial-Encoded tRNAs Change from One Plant Species to Another 246
10.2.2 Some Cytosolic tRNAs are Imported into Mitochondria 250
10.2.3 tRNA Import and Evolution 251
10.3 Why Are tRNAs Imported? 253
10.4 Use of Imported tRNA by the Mitochondrial Translational Apparatus 254
10.5 Mechanism of tRNA Mitochondrial Import 258
References 261
Chapter 11: Protein Import into Plant Mitochondria 265
11.1 Introduction 266
11.2 Mitochondrial Precursor Proteins and Cytosolic Factors 268
11.3 Mitochondrial Targeting Signals 268
11.3.1 N-Terminal Targeting Signals 270
11.3.2 Internal Targeting Signals 271
11.4 Dual Targeting Signals 271
11.5 An In-silico Picture of the Protein Import Machinery in Plants 273
11.6 Functional Studies on the Mitochondrial Protein Import Apparatus of Plants 276
11.6.1 The Outer Membrane 276
11.6.2 The Intermembrane Space 277
11.6.3 The Inner Membrane 278
11.7 Processing of Precursor Proteins and Degradation of Targeting Peptides 279
11.7.1 Processing of Precursor Proteins 279
11.7.2 Degradation of Targeting Peptides 281
11.8 Future Issues 284
References 285
Chapter 12: Mitochondrial Protein Import in Fungi and Animals 292
12.1 Introduction 293
12.2 The Multitude of Mitochondrial Targeting Signals 296
12.3 Crossing the Outer Membrane: The TOM Complex 300
12.4 Sorting and Assembly in the Outer Membrane: The SAM/TOB Complex 301
12.5 Redox-Regulated Import into the IntermembraneSpace: The MIA Pathway 304
12.6 Insertion into the Inner Membrane Via the TIM22 Complex: The Carrier Pathway 306
12.7 Import into the Matrix: The TIM23-PAM Pathway 310
12.7.1 The TIM23 Complex 310
12.7.2 The Import Motor (PAM) 313
12.8 Folding and Assembly into Active Enzyme Complexes 316
References 320
Part IV: 
Function 328
Chapter 13: Biogenesis and Supramolecular Organization of the Oxidative Phosphorylation System in Plants 329
13.1 Introduction 330
13.2 Composition and Biogenesis of Mitochondrial OXPHOS Complexes 331
13.2.1 Composition and Biogenesis of Complex I 331
13.2.2 Composition and Biogenesis of Complex II 333
13.2.3 Composition and Biogenesis of Complex III 334
13.2.4 Composition and Biogenesis of Complex IV 335
13.2.5 Composition and Biogenesis of Complex V 340
13.3 Supermolecular Organization of the Mitochondrial OXPHOS System 342
13.3.1 The I + III Supercomplex 343
13.3.2 The III + IV Supercomplex 344
13.3.3 The I + III + IV Supercomplex 344
13.3.4 The Dimeric ATP Synthase Supercomplex 345
13.4 Regulation of the Biogenesis of the OXPHOS Complexes and Supercomplexes 346
13.5 Outlook 347
References 349
Chapter 14: Mitochondrial Electron Transport and Plant Stress 358
14.1 Introduction 359
14.2 The Standard Electron Transport Chain 360
14.3 Mutations in Complexes I–IV 360
14.4 Alternative NAD(P)H Dehydrogenases 363
14.5 Alternative Oxidase 365
14.6 Coordination of Alternative NAD(P)H Dehydrogenases and the Alternative Oxidases 366
14.7 Formation of Reactive Oxygen Speciesand Its Consequences 367
14.7.1 Mitochondrial Protein Oxidation 368
14.8 Supplementary Pathways of Carbon Conversion Are Active Under Particular Stress Conditions 370
14.8.1 Respiration and Stress Tolerance 370
14.8.2 Mitochondrial d-Lactate Dehydrogenase Removes By products of Carbon Metabolism 371
14.8.3 Electron-Transfer Flavoprotein: Quinone Oxidoreductase Mediates Degradation of Amino Acids Under Carbon Starvation 371
14.8.4 Glycerol Metabolism Involves an External Glycerol-3-Phosphate Dehydrogenase 371
14.8.5 Mitochondrial Proline Degradation Readjusts the Cellular Osmotic Potential upon Alleviation of Drought Stress 372
14.9 Electron Transport Regulation During Oxygen Deprivation 373
14.10 Concluding Remarks 373
References 375
Chapter 15: Interaction Between Chloroplasts and Mitochondria: Activity, Function, and Regulation of the Mitochondrial Respiratory System during Photosynthesis 
383 
15.1 Introduction 384
15.2 Nonphotorespiratory C Metabolism in the Mitochondrial Matrix Under Light Conditions 387
15.3 Photorespiration: The Impact on the Mitochondrial and Cellular Metabolism 389
15.4 Does the TCA Cycle Have Physiologic Function(s) During Photosynthesis? 391
15.5 Light-Dependent Response of the Respiratory Chain Upregulation of the Alternative Oxidase
15.6 Function of AOX as a Dissipation System of Excess Cellular Reducing Equivalents 393
15.7 Function of Other Components in the Light 395
15.8 How is the Respiratory Gene Expression Regulated in Illuminated Leaves? 396
15.9 Posttranslational Regulation: What are the Consequences of Changes in the Mitochondrial Redox Environment in the Light? 
399 
15.10 Conclusions and Perspectives 400
References 402
Chapter 16: Plant Mitochondrial Retrograde Regulation 410
16.1 Introduction 411
16.2 MRR Overlaps with Chloroplast Retrograde Regulation 411
16.3 Mitochondrial Dysfunction and MRR 414
16.3.1 Mutations Can Cause Mitochondrial Dysfunction Resulting in MRR 416
16.3.2 Mitochondrial Dysfunction from Enzyme Inhibitors Results in MRR 417
16.4 MRR and Abiotic Stresses 418
16.4.1 Oxygen Deprivation and Sensing by Mitochondria May Result in MRR 418
16.4.2 MRR and Heat Stress 419
16.4.3 MRR and Other Abiotic Stresses 420
16.5 MRR and Biotic Stresses 420
16.5.1 The Hypersensitive Response and Plant Mitochondria 421
16.5.2 Bacterial and Fungal Elicitors Cause Mitochondrial Dysfunction, Resulting in MRR 421
16.6 Components of Plant MRR 422
16.6.1 Reactive Oxygen Species 422
16.6.2 Redox Signals in Plant MRR 424
16.6.3 Calcium and Plant MRR 425
16.6.4 Potential Protein Components of Plant MRR 426
16.7 Mitochondria, MRR and Programmed Cell Death 427
16.7.1 MRR Initiated by Plant Pathogens May Cause PCD/HR in Some Cases 427
16.7.2 MRR and the Decision Between Recovery and Cell Death 428
16.8 Multiple MRR Pathways in Plants 428
16.9 Summary 429
References 430
Chapter 17: Mitochondrial Regulation of Plant Programmed Cell Death 437
17.1 Introduction 438
17.1.1 Programmed Cell Death 438
17.1.1.1 History 438
17.1.1.2 Importance 439
17.2 The Mitochondrion and PCD in Animal Systems 441
17.2.1 Apoptosis 441
17.2.2 Autophagic Cell Death 444
17.2.3 Necrosis-Like Cell Death 446
17.3 Release Mechanisms for Mitochondrial Factors 446
17.4 Structural and Physiological Changes to Mitochondria During Plant PCD 449
17.5 Plant PCD and Apoptogenic Proteins 451
17.5.1 Cytochrome c 451
17.5.2 AIF and EndoG 452
17.6 Reactive Oxygen Species and Alternative Oxidase 452
17.7 Autophagy 454
17.8 Concluding Remarks 455
References 457
Part V: 
Repair 464
Chapter 18: Cytoplasmic Male-Sterility and Nuclear Encoded Fertility Restoration 465
18.1 Introduction 465
18.2 Definition of Cytoplasmic Male-Sterility 467
18.3 CMS-Associated Genes 468
18.4 Retrograde Signaling 469
18.4.1 Restorer-of-Fertility Genes and Restoration Mechanisms 469
18.5 CMS System 470
18.6 Somatic Hybrids 470
18.6.1 The Ogura CMS Systems 471
18.6.2 The CMS System B. napus (A. thaliana) 472
18.7 Alloplasmic, Sexual Hybrids 475
18.7.1 Zea mays CMS-T 475
18.7.2 CMS in Nicotiana 477
18.7.3 Triticum aestivum CMS 477
18.8 Does Cell Death Have a Role in CMS? 478
References 479
Chapter 19: Human Mitochondrial Mutations and Repair 488
19.1 Introduction 489
19.2 Mitochondrial Genome 491
19.3 Susceptibility of Mitochondrial DNA to Damage 492
19.4 Human Mitochondria Mutation in Aging and Disease 493
19.4.1 Aging 494
19.4.2 Diabetes Mellitus 496
19.4.3 Neurodegeneration 497
19.4.4 Cancer 498
19.5 Mitochondrial DNA Repair 499
19.5.1 DNA-Glycosylases in Mitochondria 501
19.5.2 AP Endonuclease (APE) 503
19.5.3 Mitochondrial Polymerase g 504
19.5.4 Mitochondrial DNA Ligase 505
19.6 Modulation of mtDNA Repair 505
19.7 Conclusion 507
References 508
Index 
517