Annual Plant Reviews

David C. Logan, PhD Institut de Recherche en Horticulture et Semences, Universite 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 repairA ]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 CrossA ]Talk Between Genomes: How CoA ]Evolution Shaped Plant Mitochondrial Gene Expression 33 Francoise 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: coA ]evolution makes sense 46 3.3.1 CoA ]evolution of cytoplasmic male sterility 46 3.3.2 Most Rf genes encode PPR proteins 48 3.4 CoA ]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 Gael Paszkiewicz 4.1 Introduction 67 4.2 Motility 68 4.2.1 ActinA ]mediated displacement 68 4.2.2 Microtubules 70 4.3 Number 71 4.3.1 Division 71 4.3.2 A dynaminA ]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/CluA ]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 FeA ]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 OstersetzerA ]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 CoA ]factors of the mitochondria transcription machinery 148 6.3 PostA ]transcriptional RNA processing 151 6.3.1 Trimming, RNA endA ]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 Schwarzlander 7.1 Introduction 185