Note: Intro -- Plant Mitochondria -- Preface -- Contents -- Part I: Dynamics, Genes & -- Genomes -- Chapter 1: Mitochondrial Genome Evolution in the Plant Lineage -- 1.1 Introduction -- 1.2 Land Plant Mitochondrial DNAs and Their Peculiarities -- Box 1.1 Group I and group II introns -- 1.3 Plant Mitochondrial Genomes: Completed MtDNA Sequences -- 1.4 Ongoing Gene Transfer to the Nucleus -- 1.5 Plant Mitochondrial Genomes: Structures -- 1.6 The Introns in Embryophyte Mitochondrial DNAs -- 1.7 RNA Editing -- Box 1.2 RNA editing -- 1.8 Gene Transfer Deviations: Promiscuous DNA -- 1.9 Horizontal Gene Transfer -- Box 1.3 Horizontal gene transfer -- 1.10 An Extended Perspective: What Else? -- References -- Chapter 2: Mitochondrial Dynamics -- 2.1 Introduction -- 2.2 Division -- 2.2.1 Animal and Yeast Mitochondrial Division -- 2.2.2 Plant Mitochondrial Division -- Box 2.1 The NETWORK protein -- 2.3 Fusion -- 2.3.1 Animal and Yeast Mitochondrial Fusion -- 2.3.2 Plant Mitochondrial Fusion -- 2.4 Regulation of Chondriome Structure -- 2.4.1 Temporal Regulation -- 2.4.2 Physical Regulation -- 2.5 Death -- Box 2.2 Cell death and mitochondrial morphology -- 2.6 Motility, Distribution, and Inheritance -- 2.6.1 Mitochondrial Movement and the Cytoskeleton -- 2.6.1.1 Mitochondrial Movement and Microtubules -- 2.6.1.2 Mitochondrial Movement and Actin -- Myosin -- Mechanisms Other Than Myosin-Based -- 2.6.2 Mitochondrial Motility Delivers the Organelle to the Right Places -- 2.6.3 Inheritance and Cellular Distribution -- 2.7 Conclusions -- References -- Chapter 3: Plant Mitochondrial Genomes and Recombination -- 3.1 Why Study Plant Mitochondrial Genomes? -- 3.2 The Importance of Double Strand Breaks in Plant Mitochondria -- 3.3 Plant Mitochondrial Recombination Is Under Nuclear Gene Control. , Box 3.1 The process of substoichiometric shifting (SSS) in higher plants 1/100 cells -- 3.4 The Genetic Variability of Plant Mitochondria -- 3.4.1 Large (> -- 1,000-bp) Repeated Sequences -- 3.4.2 Intermediate (ca. 50 to 500-bp) Repeated Sequences -- 3.4.3 Small (4-25 bp) Repeated Sequences -- 3.5 Other Interpretations of Mitochondrial Genetic Variation -- 3.6 Mitochondrial Recombination Influences Plant Development -- 3.7 Could Mitochondrial Status, Conditioned by Recombination, Influence Plant Adaptation? -- References -- Part II: Transcription & -- RNA Processing -- Chapter 4: Transcription in Plant Mitochondria -- 4.1 Introduction to Mitochondrial RNA Polymerases -- 4.1.1 Evolution -- Box 4.1 RNA polymerases encoded by linear plasmids -- 4.1.2 Plant Mitochondrial RNA Polymerases -- Box 4.2 Dual targeting of Rpot polymerases -- 4.2 Plant Mitochondrial Promoters -- Box 4.3 The mTERF protein family -- 4.3 Trans-Acting Factors Involved in Plant Mitochondrial Transcription -- 4.3.1 General Transcription Factor(s) -- 4.3.2 Specific Transcription Factors -- 4.4 Transcriptional Regulation of Mitochondrial Gene Expression -- References -- Chapter 5: RNA Processing and RNA Stability in Plant Mitochondria -- 5.1 Introduction -- 5.2 The Mitochondrial Transcriptome in Arabidopsis thaliana -- Box 5.1 CR-RT-PCR analysis -- 5.3 Formation of Mature Mitochondrial mRNAs in Higher Plants -- 5.4 5' End Processing of Mitochondrial mRNAs -- 5.5 Posttranscriptional Generation of 3' Ends -- 5.6 mRNA Stability -- 5.7 CMS, Posttranscriptional Processes, and PPR Proteins -- Box 5.2 Cytoplasmic male sterility -- 5.8 Mitochondrial tRNA Processing -- 5.9 Generation of Mature rRNAs in Plant Mitochondria -- 5.10 Conclusions -- Box 5.3 Main characteristics of mitochondrial mRNA processing and degradation -- References -- Chapter 6: RNA Splicing in Plant Mitochondria. , 6.1 Introduction -- Box 6.1 Examples of unusual features of Group I and Group II introns -- 6.2 Distribution of Introns in Mitochondrial Genes of Land Plants -- 6.3 Trans-Splicing Introns -- 6.4 Mechanism of Splicing in Plant Mitochondria -- 6.5 Splicing Machinery for Plant Mitochondrial Introns -- 6.6 Relationship Between Splicing and Other RNA Processing Events in Plant Mitochondria -- 6.7 Concluding Remarks -- References -- Chapter 7: RNA Editing in Higher Plant Mitochondria -- 7.1 Introduction -- Box 7.1 Other examples of RNA editing mechanisms -- 7.2 Extent and Consequences of RNA Editing in Higher Plant Mitochondria -- 7.2.1 Extent of RNA Editing -- 7.2.2 Consequences of RNA Editing -- 7.3 Functional Analysis of the Higher Plant RNA Editing Mechanism -- 7.3.1 The Use of In vitro and In Organello Systems -- 7.3.2 What Can Be Learned from Plastid RNA Editing? -- 7.3.3 Mitochondrial RNA Editing Factors -- 7.4 Evolution of RNA Editing -- 7.5 Concluding Remarks -- References -- Chapter 8: RNA-Binding Proteins Required for Chloroplast RNA Processing -- 8.1 Introduction -- 8.2 The Pentatricopeptide Repeat Proteins -- 8.2.1 Structure -- Box 8.1 The pentatricopeptide repeat (PPR) motif -- 8.2.2 Evolution -- 8.2.3 Functions of PPR Proteins -- 8.2.4 RNA Recognition by PPR Proteins -- 8.3 The Plant Organellar RNA Recognition (PORR) Family -- 8.4 Chloroplast Ribonucleoproteins -- 8.4.1 Structure, Evolution, and RNA Targets -- 8.4.2 Expression -- 8.4.3 Functions -- 8.5 Whirly Proteins -- 8.6 Chloroplast RNA Splicing and Ribosome Maturation (CRM) Proteins and Associated Factors -- 8.6.1 Evolution and Structure of the CRM Proteins -- 8.6.2 Plant CRM Proteins Are Polyvalent Splicing Factors -- 8.6.3 CRM Ribonucleoprotein Particles -- 8.6.4 CRM-Associated Factors -- 8.6.5 CRS1: Highlighting the Molecular Mechanism Behind CRM Domain Functions. , 8.7 Orphan Chloroplast RNA-Binding Proteins -- 8.8 Outlook -- References -- Part III: Translation & -- Import -- Chapter 9: The Plant Mitochondrial Proteome Composition and Stress Response: Conservation and Divergence Between Monocots and Dicots -- 9.1 Introduction -- Box 9.1 Quantitative mass spectrometry techniques -- 9.2 Overall Comparisons of Monocot and Dicot Mitochondrial Proteomes -- 9.3 Specific Examples of Conservation of Plant Mitochondrial Proteome and Function Between Monocots and Dicots -- 9.4 Specific Examples of Divergence in Plant Mitochondrial Proteome Monocots and Dicots -- 9.5 Plant Mitochondrial Proteome Responses to Abiotic Stress -- 9.6 Future Directions -- 9.6.1 Excluding Contaminants by Quantitative Analysis -- 9.6.2 In-depth Identification of Mitochondrial Proteins -- 9.6.3 Refining Quantitative Analysis of Proteome Differences of Biologic Consequence -- 9.6.4 Database Development and Access -- References -- Chapter 10: Import of RNAs into Plant Mitochondria -- 10.1 Introduction -- Box 10.1 RNA import in other compartments or organisms -- 10.2 What Are the Imported tRNAs in Photosynthetic Organisms? -- 10.2.1 The Number and Identity of Mitochondrial-Encoded tRNAs Change from One Plant Species to Another -- 10.2.2 Some Cytosolic tRNAs are Imported into Mitochondria -- 10.2.3 tRNA Import and Evolution -- 10.3 Why Are tRNAs Imported? -- 10.4 Use of Imported tRNA by the Mitochondrial Translational Apparatus -- 10.5 Mechanism of tRNA Mitochondrial Import -- References -- Chapter 11: Protein Import into Plant Mitochondria -- 11.1 Introduction -- 11.2 Mitochondrial Precursor Proteins and Cytosolic Factors -- 11.3 Mitochondrial Targeting Signals -- Box 11.1 -- 11.3.1 N-Terminal Targeting Signals -- 11.3.2 Internal Targeting Signals -- 11.4 Dual Targeting Signals. , 11.5 An In-silico Picture of the Protein Import Machinery in Plants -- Box 11.2 -- Box 11.3 -- 11.6 Functional Studies on the Mitochondrial Protein Import Apparatus of Plants -- 11.6.1 The Outer Membrane -- 11.6.2 The Intermembrane Space -- 11.6.3 The Inner Membrane -- 11.7 Processing of Precursor Proteins and Degradation of Targeting Peptides -- 11.7.1 Processing of Precursor Proteins -- 11.7.2 Degradation of Targeting Peptides -- 11.8 Future Issues -- References -- Chapter 12: Mitochondrial Protein Import in Fungi and Animals -- 12.1 Introduction -- Box 12.1 Processing of mitochondrial precursor proteins -- 12.2 The Multitude of Mitochondrial Targeting Signals -- 12.3 Crossing the Outer Membrane: The TOM Complex -- 12.4 Sorting and Assembly in the Outer Membrane: The SAM/TOB Complex -- 12.5 Redox-Regulated Import into the IntermembraneSpace: The MIA Pathway -- 12.6 Insertion into the Inner Membrane Via the TIM22 Complex: The Carrier Pathway -- 12.7 Import into the Matrix: The TIM23-PAM Pathway -- 12.7.1 The TIM23 Complex -- 12.7.2 The Import Motor (PAM) -- Box 12.2 Controversial issues concerning the Tim23-PAM pathway mechanism -- 12.8 Folding and Assembly into Active Enzyme Complexes -- References -- Part IV: Biochemistry, Regulation & -- Function -- Chapter 13: Biogenesis and Supramolecular Organization of the Oxidative Phosphorylation System in Plants -- 13.1 Introduction -- 13.2 Composition and Biogenesis of Mitochondrial OXPHOS Complexes -- 13.2.1 Composition and Biogenesis of Complex I -- 13.2.2 Composition and Biogenesis of Complex II -- 13.2.3 Composition and Biogenesis of Complex III -- 13.2.4 Composition and Biogenesis of Complex IV -- 13.2.5 Composition and Biogenesis of Complex V -- Box 13.1 Characterization of the respiratory chain by Blue native PAGE -- 13.3 Supermolecular Organization of the Mitochondrial OXPHOS System. , 13.3.1 The I + III Supercomplex.

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