Annual Plant Reviews, Plant Mitochondria

Contents......Page 7
Contributors......Page 15
Preface......Page 17
1.1 Introduction......Page 21
1.2.1 Mitochondria and prokaryotic cell division......Page 22
1.2.2 Plastids, the contractile ring, actomyosin and the loss of mitochondrial FtsZ......Page 24
1.3 Chondriome structure and organisation – the discontinuous whole......Page 26
1.4.1 Mitochondrial division......Page 28
1.4.2 Mitochondrial fusion......Page 31
1.5.1 Mitochondrial movement and the cytoskeleton......Page 34
1.5.2 Chondriome structure and the cell cycle......Page 35
1.5.3 Mitochondrial inheritance in yeast......Page 36
1.5.4 Arabidopsis friendly mitochondria mutant and the cellular distribution of mitochondria......Page 43
1.6 Other plant mitochondrial dynamics mutants......Page 44
1.7 Metabolic control of mitochondrial morphology and motility......Page 45
1.8 Concluding remarks......Page 47
References......Page 48
2.2 Unusual and dynamic nature of the plant mitochondrial genome......Page 56
2.3 Mitochondrial DNA recombination is controlled by the nucleus......Page 58
2.4 Recombination versus replication in plant mitochondrial genome dynamics......Page 61
2.5 Nuclear regulation of mitochondrial DNA maintenance......Page 63
2.6 Cellular and developmental responses to mitochondrial genome rearrangement in plants......Page 64
2.7 Plant mitochondrial genome and its adaptations......Page 65
References......Page 66
3.1 Introduction......Page 70
3.2 Identification of the pentatricopeptide repeats protein family: a key discovery toward the understanding of plant mitochondrial gene expression......Page 71
3.2.1 Structure of PPR proteins......Page 72
3.2.2 Functions of PPR proteins......Page 73
3.3.1 Conserved and variable transcription units in plant mitochondria......Page 74
3.3.2 How many different conserved and nonconserved promoter structures are there in plant mitochondria?......Page 75
3.3.3 What proteins are necessary for transcription of mitochondrial DNA?......Page 77
3.3.4 Is gene expression in plant mitochondria regulated at the transcriptional level?......Page 80
3.4.2 Cis- and trans-splicing......Page 82
3.4.3 Splicing mechanism......Page 83
3.4.4 Splicing machinery......Page 85
3.5.1 Distribution of RNA editing in the plant kingdom......Page 86
3.5.2 Function and consequences of RNA editing......Page 87
3.5.3 Mechanism and biochemistry of the RNA-editing process in higher plant mitochondria......Page 88
3.5.4 Upstream cis elements specify editing sites......Page 89
3.6.1 5' and 3' processing machinery......Page 90
3.6.2 tRNA processing......Page 91
3.6.3 rRNA processing......Page 92
3.6.4.1 Processing of 5' extremities......Page 94
3.6.4.2 Processing of 3' extremities......Page 96
3.7 Stabilization and degradation of RNA......Page 97
3.7.2 Mechanism of RNA degradation......Page 98
3.7.3 Roles of RNA degradation......Page 100
3.8.1 Translational machinery......Page 101
3.8.2 Translational control......Page 102
3.9 Concluding remarks......Page 103
References......Page 104
4.1 Introduction......Page 117
4.2 Mitochondrial-targeting signals......Page 118
4.2.1 Features of mTPs......Page 119
4.2.2 Dual-targeting peptides......Page 121
4.3 Cytosolic factors......Page 123
4.4 Sorting of precursors between mitochondria and chloroplasts......Page 125
4.5.1 Translocase of the outer membrane – the discriminating outer membrane......Page 126
4.5.3 Inner membrane – a tale of two Tims and more......Page 129
4.6 Proteolytic events......Page 132
4.6.1.1 Integration of plant MPP into the cytochrome bc1 complex of the respiratory chain......Page 133
4.6.1.2 Catalysis and substrate specificity of MPP......Page 134
4.6.2 Mitochondrial intermediate peptidase, MIP......Page 136
4.6.3 Inner membrane peptidase, IMP......Page 137
4.6.4.1 Identification, intracellular localization and expression of PreP......Page 138
4.6.4.2 Catalysis and substrate specificity of PreP......Page 140
4.6.5 A membrane-bound ATP-dependent protease, FtsH......Page 141
4.6.6 Lon-like ATP-dependent proteases......Page 142
4.6.7 ATP-dependent Clp protease......Page 143
4.6.8 An integral membrane Rhomboid protease......Page 144
4.7 Evolution of protein import components......Page 145
4.9 Concluding remarks......Page 147
References......Page 148
5.1 Introduction......Page 161
5.2.1 Mitochondrial Fe–S clusters biogenesis......Page 163
5.2.2 Late steps of heme B synthesis......Page 165
5.2.3 Heme A synthesis......Page 167
5.3.1 Complex I assembly......Page 168
5.3.2 Cytochrome c maturation is required for the biogenesis of complex III......Page 169
5.3.3 Complex IV assembly......Page 170
5.3.4 Complex V assembly......Page 172
5.4.1 Nuclear co-ordination of the expression of electron transport chain genes......Page 173
5.4.2 Co-ordination between mitochondrial and nuclear gene expression......Page 175
5.5.1 Clues for plant mitochondrial retrograde signalling......Page 178
5.5.2 Potential components of retrograde-signalling pathways......Page 180
5.6 Concluding remarks......Page 181
References......Page 182
6.2 Structure and function of OXPHOS complexes I–V......Page 191
6.2.3 Complex III......Page 192
6.3.1 Solid-state versus fluid-state model......Page 193
6.3.2 Composition of OXPHOS supercomplexes in plants......Page 196
6.3.3 Structure of OXPHOS supercomplexes in plants......Page 197
6.3.4 Function of OXPHOS supercomplexes in plants......Page 198
6.4 Concluding remarks......Page 199
References......Page 200
7.2.1 The standard ETC complexes......Page 205
7.2.2 Other “standard” ETC enzymes......Page 207
7.4.1 Basic properties......Page 208
7.4.3 Alamethicin is a useful tool to study respiration in intact cells and isolated mitochondria......Page 210
7.5.2 The reduction level of NAD(P)......Page 211
7.5.4 Transhydrogenase......Page 212
7.6.1 Minimising ROS production......Page 213
7.6.2.1 ROS removal by SOD and (possibly) catalase......Page 215
7.6.2.3 Glutathione peroxidases......Page 216
7.7 Mitochondrial DNA and lipid oxidation......Page 217
7.7.2 Lipid oxidation......Page 218
7.8.2 Identification of oxidised mitochondrial proteins......Page 219
7.8.3 Enzymes interacting with ROS as part of their function......Page 222
7.9 Fate of oxidised proteins......Page 223
7.10 How to prevent the transfer of oxidative damage to the next generation?......Page 224
References......Page 225
8.1 Introduction......Page 232
8.2.1 Enzymes of the TCA cycle......Page 233
8.2.1.1 Pyruvate dehydrogenase complex......Page 234
8.2.1.2 NAD-malic enzyme......Page 238
8.2.1.4 Aconitase......Page 239
8.2.1.5 Isocitrate dehydrogenase......Page 240
8.2.1.6 2-oxoglutarate dehydrogenase complex......Page 242
8.2.1.8 Succinate dehydrogenase......Page 243
8.2.1.9 Fumarase......Page 244
8.2.1.10 Malate dehydrogenase......Page 245
8.3.1 Complex I......Page 246
8.3.2 Complex II......Page 247
8.3.5 Complex V......Page 248
8.3.7 Additional NADH-dehydrogenases......Page 249
8.4 Carriers......Page 251
8.5.1 Cysteine......Page 253
8.5.3 Glycine......Page 254
8.5.4 Branched-chain amino acids......Page 256
8.6.2 Biotin......Page 257
8.6.4 Folate......Page 259
8.6.6 Lipids......Page 261
8.7.1 Respiratory activity in the light......Page 262
8.7.2 Provision of mitochondrial ATP to support cytosolic sucrose synthesis......Page 264
8.7.3 A role for the reactions converting acetyl CoA to  A-ketoglutarate in nitrogen assimilation......Page 265
8.7.4 Export of redox equivalents to support photorespiration......Page 268
8.7.5 Improved photosynthetic performance by modification of TCA cycle activity......Page 269
8.7.6 Mitochondrial metabolism and floral development......Page 273
8.7.7 Role of mitochondrial metabolism in root nutrient uptake......Page 274
8.7.8 Metabolic activity of mitochondria during climacteric fruit ripening......Page 275
8.8 Concluding remarks – future prospects for improved understanding of the interaction between mitochondrial and extra-mitochondrial metabolism......Page 276
References......Page 277
9.1 Introduction......Page 298
9.2.1 The problem of identifying CMS genes......Page 300
9.2.2 The origin of CMS genes and its consequences......Page 303
9.2.3 The population geneticists’ view of CMS......Page 305
9.3.1 Mitochondria and plant sexual reproduction......Page 306
9.3.2 T-URF13 and possible mechanisms for maize Texas sterility plus other CMS gene products and their characteristics......Page 309
9.4.1 Rf genes: genetic characteristics and molecular effects......Page 310
9.5 Restorers as PPR proteins, biochemical and evolutionary implications......Page 314
9.6 Concluding remarks......Page 316
References......Page 317
10.1 Introduction......Page 328
10.2 Programmed cell death......Page 329
10.3 Death programmes......Page 330
10.4 The mitochondrion and mammalian apoptosis......Page 331
10.5 Mitochondrial structural and physiological changes during PCD......Page 334
10.6.1 Cytochrome c and plant PCD......Page 337
10.7 Release mechanisms for mitochondrial factors......Page 339
10.7.1 Bcl-like proteins and plant PCD......Page 340
10.7.2 The PTP and plant PCD......Page 341
10.8 Reactive oxygen species......Page 344
10.9 Alternative oxidase......Page 346
10.10 The involvement of de novo protein synthesis in plant PCD......Page 347
10.11 Concluding remarks......Page 348
References......Page 349
Index......Page 355
The colour plate section follows page 110......Page 363