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Contents Contributors 000 Preface 000 1 Mitochondrial dynamics: the control of mitochondrial shape, size, number, motility, and cellular inheritance 000 Iain Scott and David C. Logan 1.1 Introduction 1.2 Endosymbiosis and mitochondrial evolution 1.2.1 Mitochondria and prokaryotic cell division 1.2.2 Plastids, the contractile ring, actomyosin, and the loss of mitochondrial FtsZ 1.3 Mitochondrial chondriome structure and organisation ¿ the discontinuous whole 1.4 Control of mitochondrial number, size, and gross morphology 1.4.1 Mitochondrial division 1.4.2 Mitochondrial fusion 1.5 Mitochondrial movement and cellular inheritance 1.5.1 Mitochondrial movement and the cytoskeleton 1.5.2 Chondriome structure and the cell cycle 1.5.3 Mitochondrial inheritance in yeast 1.5.4 The Arabidopsis friendly mitochondria mutant and the cellular distribution of mitochondria 1.6 Other plant mitochondrial dynamics mutants 1.7 Metabolic control of mitochondrial morphology and motility 1.8 Concluding remarks 2 The unique biology of mitochondrial genome instability in plants, 000 Sally A. Mackenzie 2.1 Introduction 2.2 The unusual and dynamic nature of the plant mitochondrial genome 2.3 Mitochondrial DNA recombination is controlled by the nucleus 2.4 Recombination versus replication in plant mitochondrial genome dynamics 2.5 Nuclear regulation of mitochondrial DNA maintenance 2.6 Cellular and developmental responses to mitochondrial genome rearrangement in plants 2.7 The plant mitochondrial genome and its adaptations 3 Expression of the plant mitochondrial genome 000 Dominique Gagliardi and Stefan Binder 3.1 Introduction 3.2 Identification of the PPR protein family: a key discovery towards the understanding of plant mitochondrial gene expression 3.2.1 Structure of PPR proteins 3.2.2 Functions of PPR proteins 3.3 Transcription in higher plant mitochondria 3.3.1 Conserved and variable transcription units in plant mitochondria 3.3.2 How many different conserved and non-conserved promoter structures are there in plant mitochondria? 3.3.3 What proteins are necessary for transcription of mitochondrial DNA? 3.3.4 Is gene expression in plant mitochondria regulated at the transcriptional level? 3.4 Splicing 3.4.1 Intron types 3.4.2 Cis- and trans splicing 3.4.3 Splicing mechanism 3.4.4 Splicing machinery 3.5 Exchange of nucleotide identity by RNA editing 3.5.1 Distribution of RNA editing in the plant kingdom 3.5.2 Function and consequences of RNA editing 3.5.3 Mechanism and biochemistry of the RNA editing process in higher plant mitochondria 3.5.4 Upstream cis elements specify editing sites 3.6 5' and 3' processing of plant mitochondrial transcripts 3.6.1 5' and 3' processing machinery 3.6.2 tRNA processing 3.6.3 rRNA processing 3.6.4 mRNA processing 3.6.4.1 Processing of 5' extremities 3.6.4.2 Processing of 3' extremities 3.7 Stabilization and degradation of RNA 3.7.1 Cis and trans elements stabilizing mRNA 3.7.2 Mechanism of RNA degradation 3.7.3 Roles of RNA degradation 3.8 Translation and post-translational control 3.8.1 Translational machinery 3.8.2 Translational control 3.8.3 Post-translational control 3.9 Concluding remarks 4 Import of nuclear encoded mitochondrial proteins 000 Elzbieta Glaser and James Whelan 4.1 Introduction 4.2 Mitochondrial targeting signals 4.2.1 The features of mitochondrial targeting peptides 4.2.2 Dual targeting peptides 4.3 Cytosolic factors 4.4 Sorting of precursors between mitochondria and chloroplasts 4.5 Translocation machinery 4.5.1 Translocase of the Outer Membrane - The Discriminating Outer Membrane 4.5.3 The Inner Membrane - A Tale of Two Tims and More 4.5.2 The Rediscovered Intermembrane Space 4.5.3 The Inner Membrane - A Tale of Two Tims and More 4.5.4 The Matrix - The Engine Room 4.5 Proteolytic events 4.5.1 Mitochondrial Processing Peptidase, MPP 4.5.1.1 Integration of plant MPP into the cytochrome bc1 complex of the respiratory chain 4.5.1.2 Catalysis and substrate specificity of MPP 4.5.2 Mitochondrial Intermediate Peptidase, MIP 4.5.3 Inner Membrane Peptidase, IMP 4.5.4 The mitochondrial peptidasome, the presequence protease PreP 4.5.4.1 Identification, intracellular localization, and expression of PreP 4.5.4.2 Catalysis and substrate specificity of PreP 4.5.5 A membrane-bound ATP-dependent protease, FtsH 4.5.6 Lon-like ATP-dependent proteases 4.5.7 The ATP-dependent Clp protease 4.5.8 An integral membrane serine protease Rhomboid 4.6 Evolution of protein import components 4.7 Genomic perspective of mitochondrial protein import components 4.8 Concluding remarks 5 Mitochondrial respiratory complex biogenesis: communication, gene expression and assembly 000 Philippe Giegé 5.1 Introduction 5.2 Biogenesis of prosthetic groups essential for respiration 5.2.1 Mitochondrial iron-sulphur clusters biogenesis 5.2.2 Late steps of heme B synthesis 5.2.3 Heme A synthesis 5.3 Mitochondrial respiratory complexes assembly 5.3.3 Complex I assembly 5.3.4 Cytochrome c maturation is required for the biogenesis of complex III 5.3.5 Complex IV assembly 5.3.6 Complex V assembly 5.4 Gene expression for the biogenesis of mitochondrial respiratory complexes 5.4.1 Nuclear coordination of the expression of electron transport chain genes 5.4.2 Coordination between mitochondrial and nuclear gene expression 5.5 Mitochondria-nucleus crosstalk 5.5.1 Clues for plant mitochondrial retrograde signalling 5.5.2 Potential components of retrograde signalling pathways 5.6 Concluding remarks 6 Supramolecular structure of the OXPHOS system in plants 000 Jesco Heinemeyer, Natalya V. Dudkina, Egbert J. Boekema and Hans-Peter Braun 6.1 Introduction 6.2 Structure and Function of OXPHOS complexes I-V 6.2.1 Complex I 6.2.2 Complex II 6.2.3 Complex III 6.2.4 Complex IV 6.2.5 Complex V 6.3. Supramolecular organization of the OXPHOS system 6.3.1. Solid-state versus fluid-state model 6.3.2 Composition of OXPHOS supercomplexes in plants 6.3.3. Structure of OXPHOS supercomplexes in plants 6.3.4. Function of OXPHOS supercomplexes in plants 6.4 Concluding remarks 7 Mitochondrial electron transport and oxidative stress 000 Ian M. Møller 7.1 Introduction 7.2 The standard electron transport chain 7.2.1 The standard ETC complexes 7.2.1.1 Complex I 7.2.1.2 Complex II 7.2.1.3 Complex III 7.2.1.4 Complex IV 7.2.2 Other standard ETC enzymes 7.3 The alternative oxidase (AOX) 7.4 NAD(P)H dehydrogenases 7.4.1 Basic properties 7.4.2 Physiology of the NAD(P)H dehydrogenases 7.4.3 Alamethicin is a useful tool to study respiration in intact cells and isolated mitochondria 7.5 Substrates for the NAD(P)H dehydrogenases 7.5.1 NAD(P) transport, synthesis and degradation 7.5.2 The reduction level of NAD(P) 7.5.3 Free vs bound NADH 7.5.4 Transhydrogenase 7.6 Oxidative stress ¿ ROS turnover 7.6.1 Minimizing ROS production 7.6.2 Removal or detoxification of ROS 7.6.2.1 ROS removal by SOD and (possibly) catalase 7.6.2.2 The ascorbate/glutathione cycle 7.6.2.3 Glutathione peroxidases 7.6.2.4 The thioredoxin and thioredoxin reductase system 7.6.2.5 Peroxiredoxin 7.7 Mitochondrial DNA and lipid oxidation 7.7.1 DNA oxidation 7.7.2 Lipid oxidation 7.8 Mitochondrial protein oxidation 7.8.1 Reaction with ROS 7.8.2 Identification of oxidised mitochondrial proteins 7.8.3 Enzymes interacting with ROS as part of their function 7.8.4 Conjugation with products of PUFA oxidation 7.9 Fate of oxidised proteins 7.10 How to prevent the transfer of oxidative damage to the next generation? 7.11 Concluding remarks 8 Mitochondrial metabolism 000 Adriano Nunes-Nesi and Alisdair R. Fernie 8.1 Introduction 8.2 Metabolic pathways of the mitochondria 8.2.1 Enzymes of the TCA cycle 8.2.1.1 Pyruvate dehydrogenase complex 8.2.1.2 NAD-malic enzyme 8.2.1.3 Citrate synthase 8.2.1.4 Aconitase 8.2.1.5 Isocitrate Dehydrogenase 8.2.1.6 2-oxoglutarate dehydrogenase complex 8.2.1.7 Succinyl-CoA ligase 8.2.1.8 Succinate dehydrogenase 8.2.1.9 Fumarase 8.2.1.10 Malate dehydrogenase 8.3 Mitochondrial electron transport 8.3.1 Comlpex I 8.3.2 Complex II 8.3.3 Complex III 8.3.4 Complex IV 8.3.5 Complex V 8.3.6 Alternative oxidase 8.3.7 Additional NADH-dehydrogenases 8.4 Carriers 8.5 Amino Acid Metabolism 8.5.1 Cysteine 8.5.2 Proline 8.5.3 Glycine 8.5.4 Branched-chain amino acids 8.6 Biosynthesis of vitamins and lipids 8.6.1 Lipoic acid 8.6.2 Biotin 8.6.3 Thiamine 8.6.4 Folate 8.6.5 Isoprenoids 8.6.6 Lipids 8.7 The role of mitochondrial metabolism in biological processes 8.7.1 Respiratory activity in the light 8.7.2 Provision of mitochondrial ATP to support cytosolic sucrose synthesis 8.7.3 A role for the reactions converting acetyl CoA to ?-ketoglutarate in nitrogen assimilation 8.7.4 The export of redox equivalents to support photorespiration 8.7.5 Improved photosynthetic performance by modification of TCA cycle activity 8.7.6 Mitochondrial metabolism and floral development 8.7.7 Role of mitochondrial metabolism in root nutrient uptake 8.7.8 Metabolic activity of mitochondria during climacteric fruit ripening 8.8 Concluding remarks - future prospects for improved understanding of the interaction between mitochondrial and extra-mitochondrial metabolism 9 Cytoplasmic male sterilities and mitochondrial gene mutations in plants 000 Françoise Budar and Richard Berthomé 9.1 Introduction 9.2 The identification and characteristics of CMS genes 9.2.1 The problem of identifying CMS genes 9.2.2 The origin of CMS genes and its consequences 9.3.3 CMS and PCD 9.2.3 The population geneticists¿ view of CMS 9.3 Current hypotheses concerning sterility mechanisms and the role of mitochondria in plant reproduction. 9.3.1 Mitochondria and plant sexual reproduction 9.3.2 T-URF13 and possible mechanisms for maize Texas sterility plus other CMS gene products and their characteristics 9.4 The restoration of fertility by nuclear genes 9.4.1 Rf genes: genetic characteristics and molecular effects 9.5 Restorers as PPR proteins, biochemical and evolutionary implications 9.6 Concluding remarks 10 The mitochondrion and plant programmed cell death 000 Mark Diamond & Paul F. McCabe 10.1 Introduction 10.2 Programmed cell death 10.3 Death programmes 10.4 The mitochondrion and mammalian apoptosis 10.5 Mitochondrial structural and physiological changes during PCD 10.6 Roles of mitochondrial apoptogenic proteins in plant PCD 10.6.1 Cytochrome c and plant PCD 10.6.2 AIF and endo G 10.7 Release mechanisms for mitochondrial factors 10.7.1 Bcl-like proteins and plant PCD 10.7.2 The PTP and plant PCD 10.8 Reactive oxygen species 10.9 Alternative oxidase 10.10 The involvement of de novo protein synthesis in plant PCD 10.11 Concluding remarks Index 000
Library of Congress Subject Headings for this publication:
Plant mitochondria.