Title Details

David C. Logan, PhD
Institut de Recherche en Horticulture et Semences, Université d'Angers, France.

List of Contributors xv

Preface xvii

1 Bioblasts, Cytomikrosomen and Chondriosomes: A Short Incomplete History of Plant Mitochondrial Research 1
David C. Logan and Iain Scott

1.1 Discovery 1

1.2 Complexity of nomenclature 2

1.2.1 Discoveries of mitochondria in plants 2

1.3 Mitochondrial are dynamic 3

1.4 Mitochondrial function and outputs 4

1.4.1 Vital staining of mitochondria with Janus green B and identification of mitochondria as sites of redox 5

1.4.2 Special features of plant mitochondria 6

1.5 Mitochondrial DNA 6

1.5.1 Mitochondria, photosynthesis and carbon cycling 7

1.5.2 A trigger for death 7

1.6 Known knowns, known unknowns and unknown unknowns of mitochondrial biology 8

References 9

2 Mitochondrial DNA Repair and Genome Evolution 11
Alan C. Christensen

2.1 Plant mitochondrial genomes are large and variable 11

2.1.1 Low mutation rates in genes 11

2.1.2 Genome Organization 12

2.1.3 Genome replication 13

2.2 The mutational burden hypothesis 13

2.2.1 Problems with the MBH and mutation rate measurements 13

2.3 DNA repair]based hypothesis 16

2.4 Additional mechanisms of DNA repair 19

2.4.1 Mismatch repair and MSH1 20

2.4.2 Nucleotide excision repair 22

2.5 Outcomes of DNA repair 22

2.6 How repair processes affect genome evolution 23

2.7 Unanswered questions 24

Acknowledgements 25

References 26

3 The Cross]Talk Between Genomes: How Co]Evolution Shaped Plant Mitochondrial Gene Expression 33
Françoise Budar and Hakim Mireau

3.1 Introduction 33

3.2 Evidence showing the versatility of factors involved in plant mitochondria gene expression 35

3.2.1 Transcription 35

3.2.2 RNA maturation 38

3.2.3 RNA editing 41

3.2.4 Intron splicing 44

3.3 Mitochondrial gene expression: co]evolution makes sense 46

3.3.1 Co]evolution of cytoplasmic male sterility 46

3.3.2 Most Rf genes encode PPR proteins 48

3.4 Co]evolution scenarios 50

3.5 Conclusion and perspectives 54

References 54

4 The Dynamic Chondriome: Control of Number, Shape, Size and Motility of Mitochondria 67
David C. Logan and Gaël Paszkiewicz

4.1 Introduction 67

4.2 Motility 68

4.2.1 Actin]mediated displacement 68

4.2.2 Microtubules 70

4.3 Number 71

4.3.1 Division 71

4.3.2 A dynamin]independent division mechanism? 80

4.3.3 Fusion 81

4.4 The chondriostat: mitochondrial dynamics during development and following modification of cell environment 86

4.5 Mitochondrial quality control and regulation of dynamics to enable selective degradation of mitochondria 88

4.5.1 The mitophagy apparatus 89

4.5.2 FRIENDLY/Clu]type proteins 92

4.6 Case study: mitochondrial dynamics during germination 94

4.6.1 The germination process 94

4.6.2 The chondriome during germination 96

4.7 Conclusions 99

Acknowledgements 99

References 100

5 Metal Homeostasis in Plant Mitochondria 111
Gianpiero Vigani and Marc Hanikenne

5.1 Introduction 111

5.2 Iron 114

5.2.1 Heme and Fe]S clusters 114

5.2.2 Fe binding proteins 117

5.2.3 Fe transport 119

5.3 Copper 121

5.4 Zinc 123

5.5 Manganese 125

5.6 Trace metals in plant mitochondria 128

5.7 Metallome perturbation within mitochondria 129

5.8 Conclusions 132

Acknowledgements 132

References 133

6 RNA Metabolism and Transcript Regulation 143
Michal Zmudjak and Oren Ostersetzer]Biran

6.1 Introduction 143

6.2 The mitochondrial transcription machinery 145

6.2.1 Analyses of mitochondrial promoter regions 146

6.2.2 RNA polymerases 147

6.2.3 Co]factors of the mitochondria transcription machinery 148

6.3 Post]transcriptional RNA processing 151

6.3.1 Trimming, RNA end]processing and decay in plant mitochondria 151

6.3.2 RNA editing 155

6.3.3 Splicing of mitochondrial group II introns 159

Acknowledgements 168

References 168

7 Mitochondrial Regulation and Signalling in the Photosynthetic Cell: Principles and Concepts 185
Iris Finkemeier and Markus Schwarzländer

7.1 Introduction 185

7.2 Regulation of protein functions within plant mitochondria 187

7.2.1 Regulation of transcription and translation within mitochondria 188

7.2.2 Regulation of nuclear gene expression 189

7.2.3 Regulation of cytosolic translation and protein import into mitochondria 192

7.2.4 Regulation of protein turnover within mitochondria 194

7.2.5 Regulation of function and activity of mitochondrial proteins by post]translational modifications and small molecules 195

7.2.6 Regulation of mitochondrial number and organization as set by motility, fission, fusion and mitophagy 207

7.3 Integration of chloroplast and mitochondrial regulation and signalling 209

7.3.1 Mitochondria and chloroplasts make up a joint operational unit in the light 209

7.3.2 Operational integration of mitochondria and chloroplasts requires interdependent regulation 210

7.3.3 Does the concept of ‘mitochondrial retrograde signalling’ need rethinking for green plant cells? 211

Acknowledgements 214

References 214

8 Mitochondrial Biochemistry: Stress Responses and Roles in Stress Alleviation 227
Richard P. Jacoby, A. Harvey Millar and Nicolas L. Taylor

8.1 Introduction 227

8.2 Plant mitochondrial oxidative stress 228

8.2.1 Accumulation of ROS in mitochondria 228

8.2.2 ROS]induced lipid peroxidation in mitochondria 230

8.2.3 Metallome changes during oxidative stress 231

8.2.4 Proteome changes during oxidative stress 232

8.3 Plant mitochondrial roles in harsh environments and in a changing climate 234

8.3.1 Mitochondrial roles under temperature stress 236

8.3.2 The roles of mitochondria in mediating drought tolerance 237

8.3.3 Mitochondrial respiration and salinity stress 240

8.4 Stress]dissipating roles of plant mitochondrial metabolism and products 243

8.4.1 Mitochondrial impact on photosynthetic functions during environmental stress 243

8.4.2 Root]specific mitochondrial processes mediating tolerance to unfavourable soil conditions 245

8.4.3 Cellular survival during and following stress requires mitochondrial metabolism and its products 246

8.5 Future perspectives 247

Acknowledgements 247

References 247

9 Ecophysiology of Plant Respiration 269
Néstor Fernández Del]Saz and Miquel Ribas]Carbo

9.1 Introduction 269

9.2 What is respiration? 269

9.3 The CO2/O2 paradigm 271

9.4 Oxygen consumption 273

9.4.1 Measuring oxygen uptake of organs 273

9.4.2 The regulation of oxygen uptake 274

9.4.3 Plant respiration at the ecosystem scale 277

9.5 CO2 production 278

9.5.1 Measuring organ CO2 production 278

9.5.2 IRGA 279

9.5.3 Environmental effects on CO2 measurement 280

9.5.4 Plant and ecosystem scale 281

9.5.5 Open top chambers (small]community studies) 281

9.5.6 Free]air CO2 enrichment 282

9.6 Carbon balance 283

9.6.1 Ecosystem carbon balance (eddies) 283

9.6.2 Global carbon balance 284

References 284

10 Photorespiration – Damage Repair Pathway of the Calvin–Benson Cycle 293
Hermann Bauwe

10.1 Introduction 293

10.2 Photorespiration prevents potential damage from a side reaction of RuBP carboxylase 295

10.3 Plant photorespiratory carbon metabolism 296

10.3.1 Glycolate 2]phosphate becomes dephosphorylated to glycolate 297

10.3.2 Glycolate is converted into glycine in the peroxisome 300

10.3.3 Glycolate oxidation 301

10.3.4 H2O2 degradation 302

10.3.5 Transamination of glyoxylate to glycine 303

10.3.6 Mitochondrial reactions combine two molecules of glycine to form serine and CO2 305

10.3.7 Back in the peroxisome, hydroxypyruvate is produced from serine and becomes oxidized to glycerate 316

10.3.8 Back in the chloroplast, 3PGA is formed to replenish the Calvin–Benson cycle 317

10.4 Interaction of photorespiration with other aspects of metabolism 318

10.4.1 Plant photorespiratory nitrogen cycle 318

10.4.2 TCA cycle and oxidative phosphorylation 321

10.5 Improving photosynthesis 322

Acknowledgement 323

References 324

11 Mitochondria and Cell Death 343
Olivier van Aken

11.1 Introduction 343

11.2 Conservation of mitochondrial PCD pathways in plants 344

11.3 The role of mitochondrial ROS in plant PCD 347

11.4 Non]ROS]related molecules and plant PCD 350

11.5 An update on the mitochondrial permeability transition pore 351

11.6 Senescence, autophagy and PCD 354

11.7 Interactions between mitochondria and chloroplasts during PCD 355

11.8 Conclusions 357

Acknowledgements 359

References 360

Index