Note: Intro -- Preface -- Contents -- Contributors -- Part I -- Genetic Material and its Expression -- Chapter 1 -- Chloroplast Gene Expression-RNA Synthesis and Processing -- 1.1 Introduction -- 1.2 RNA Synthesis -- 1.2.1 The Plastid-Encoded Plastid RNA Polymerase (PEP) is a Bacteria-Type Multisubunit RNA Polymerase -- 1.2.2 PEP Promoters -- 1.2.3 The Nuclear-Encoded Plastid RNA Polymerase (NEP) is Represented by Phage-Type RNA Polymerases -- 1.2.4 NEP Promoters -- 1.2.5 Division of Labor among Different Plastid RNA Polymerases -- 1.3 RNA Processing -- 1.3.1 Chloroplast RNA Splicing -- 1.3.1.1 Chloroplast Introns and Factors -- 1.3.1.2 Regulation of Chloroplast RNA Splicing -- 1.3.2 Chloroplast RNA Editing -- 1.3.2.1 Chloroplast RNA Editing Sites and Factors -- 1.3.2.2 Regulation of Chloroplast RNA Editing -- 1.3.3 RNA Cleavage and Degradation -- 1.3.3.1 Chloroplast RNases -- 1.3.3.2 Intercistronic mRNA Processing -- 1.3.3.3 Regulation of RNA Degradation -- 1.3.4 RNA Processing: Outlook -- References -- Chapter 2 -- Chloroplast Gene Expression-Translation -- 2.1 Introduction -- 2.2 Technical Considerations for Measuring Translational Activities in Chloroplasts -- 2.2.1 Genetic Approaches -- 2.2.1.1 Model Organisms -- 2.2.1.2 Chloroplast Reporter Genes -- 2.2.2 Measurement of in vivo Protein Synthesis -- 2.2.2.1 Pulse Labelling of Proteins -- 2.2.2.2 Polysomal Loading -- 2.2.3 Reconstituted Systems -- 2.2.3.1 In Vitro Translation Systems -- 2.2.3.2 RNA Binding Assays -- 2.3 Constituents of the Chloroplast Translational Apparatus -- 2.3.1 Basic Elements and Factors -- 2.3.1.1 Chloroplast tRNAs and Codon Usage -- 2.3.1.2 Chloroplast Ribosomes and General Translation Factors -- 2.3.1.3 Shine-Dalgarno Sequences and Start Codon Recognition -- 2.3.2 Gene Specific Elements and Factors for Translation Initiation. , 2.3.2.1 Cis-acting Signals on Chloroplast RNAs -- 2.3.2.2 Nucleus-Encoded Factors for Chloroplast Translation -- 2.4 Regulatory Principles of Chloroplast Translation -- 2.4.1 Regulation by Light and Redox/Metabolic Status -- 2.4.1.1 psbA mRNA Translation -- 2.4.1.2 psbD mRNA Translation -- 2.4.1.3 rbcL mRNA Translation -- 2.4.1.4 psaB mRNA Translation -- 2.4.2 Regulation of Translation via Interconnected Steps of Gene Expression -- 2.5 Spatial Organization of Chloroplast Translation -- 2.6 Conclusions and Future Perspectives -- References -- Chapter 3 -- The Chloroplast Genome and Nucleo-Cytosolic Crosstalk -- 3.1 Introduction -- 3.2 Nucleus-Encoded Trans-Acting Factors Involved in Chloroplast Gene Expression -- 3.2.1 Chloroplast Transcription Factors -- 3.2.2 Factors Involved in Post-Transcriptional Steps of Chloroplast Gene Expression -- 3.2.3 CES Control -- 3.2.4 Redox Control of Post-Transcriptional Steps of Chloroplast Gene Expression -- 3.3 Retrograde Signaling -- 3.3.1 Role of Tetrapyrroles in Retrograde Signaling -- 3.3.2 Plastid Protein Synthesis and Retrograde Signaling -- 3.3.3 Chloroplast Redox Changes and Retrograde Signaling -- 3.3.4 Reactive Oxygen Species Involved in Retrograde Signaling -- 3.3.5 Additional Metabolites Involved in Retrograde Signaling during Stress Responses -- 3.3.6 Repressible Chloroplast Gene Expression in Chlamydomonas -- 3.4 Conclusions and Perspectives -- References -- Part II -- Plastid Differentiation -- Chapter 4 -- An Overview of Chloroplast Biogenesis and Development -- 4.1 Introduction -- 4.2 Chloroplast Biogenesis -- 4.3 Plastidic and Nuclear Factors Required for Chloroplast Biogenesis -- 4.3.1 Nuclear Transcription -- 4.3.2 Chloroplast Gene Transcription and Translation -- 4.3.3 Protein Import and Processing -- 4.3.4 Pigment Biosynthesis -- 4.3.5 Retrograde Signalling -- 4.3.6 Chloroplast Division. , 4.4 Temporal and Cellular Factors Required for Chloroplast Biogenesis and Development -- 4.5 Future Directions -- References -- Chapter 5 -- Dynamic Architecture of Plant Photosynthetic Membranes -- 5.1 Introduction -- 5.2 Overall Thylakoid Architecture -- 5.2.1 Structural Organization of Grana Thylakoids -- 5.2.1.1 Grana Diameter -- 5.2.1.2 Grana Distribution in Chloroplasts -- 5.2.1.3 Transversal Grana Structure -- 5.2.2 Flexibility of the Grana Architecture -- 5.2.2.1 Classification of Structural Changes in the Grana Architecture -- 5.2.2.2 Lateral Changes in Grana Diameter (Fig. 5.1b) -- 5.2.2.3 Swelling of Thylakoid Lumen (Fig. 5.1c) -- 5.2.2.4 Vertical Destacking of Grana (Fig. 5.1d) -- 5.3 The Supramolecular Level -- 5.3.1 Macromolecular Crowding -- 5.3.2 Disordered Versus Ordered -- 5.3.3 Functional Significance of Protein Ordering -- 5.3.4 Stroma Lamellae -- 5.4 Outlook -- References -- Chapter 6 -- Plastid Division -- 6.1 Introduction -- 6.2 Placement of the Plastid Division Site -- 6.2.1 Many Proteins are Involved in the Choice of the Division Site -- 6.2.2 How Do Proteins Involved in the Choice of the Division Site Work Together? -- 6.3 Assembly and Dynamics of the FtsZ Ring -- 6.3.1 Z-ring Assembly Requires Two Isoforms of FtsZ -- 6.3.2 Opposing Roles of ARC6 and PARC6 on Z-Ring Formation -- 6.3.3 Chaperone-Regulation of Z-Ring Assembly/Maintenance -- 6.4 Assembly of the Plastid Division Machinery -- 6.4.1 The Plastid Dividing Rings -- 6.4.2 PDV1, PDV2 and Dynamin Recruitment to the Division Site -- 6.5 Constriction and Separation of Chloroplasts -- 6.5.1 Force Generation by the Stromal Plastid Division Machinery -- 6.5.2 Force Generation by the Cytosolic Plastid Division Machinery -- 6.6 Regulation of Plastid Division -- 6.6.1 Regulation During Cell Proliferation -- 6.6.2 Plastid Division and Plastid DNA Replication. , 6.6.3 Plastid Division Is Regulated by Cell Differentiation, and Cell Expansion -- 6.6.4 Chloroplast Division Is Regulated by Exogenous Cues -- References -- Chapter 7 -- Stromules -- 7.1 Introduction -- 7.2 Initial Observations of Stromule-Like Structures in Plants -- 7.2.1 Stromules in Different Cells and Tissues -- 7.2.2 Initial Observations of Stromules in Virus Infected Tissue -- 7.2.3 Stromules are Dynamic -- 7.2.4 Extension and Retraction Rates -- 7.3 Visualization of Stromules -- 7.3.1 Differential Interference Contrast (DIC) Imaging of Stromules -- 7.3.2 Fluorescent Protein Markers and Confocal Microscopy -- 7.3.3 Transmission Electron Microscopy (TEM) and Cryo-fixation of Stromules -- 7.4 Origin, Formation and Regulation of Stromule Formation -- 7.4.1 Chloroplast Envelope -- 7.4.2 Actin and Microtubule Requirements -- 7.5 Induction and Regulation of Stromules -- 7.5.1 Abiotic Stress Responses -- 7.5.2 Biotic Stress Defense Response -- 7.5.3 ABA and H2O2-Mediated Induction of Stromules -- 7.6 Putative Functions of Stromules -- 7.6.1 Increased Chloroplast Surface Area -- 7.6.2 Intra- and Inter-organelle Trafficking -- 7.6.3 Signaling -- 7.6.4 Starch Granule Formation -- 7.7 Future Insights -- References -- Chapter 8 -- The Apicoplast: A Parasite's Symbiont -- 8.1 Introduction -- 8.1.1 What are Apicomplexans? -- 8.1.2 Obligate Intracellular Parasites with a Plastid -- 8.2 Apicoplast Origin and Evolution -- 8.2.1 Metamorphosis of an Alga -- 8.2.2 The Origin of the Apicoplast: The Red Versus Green Debate -- 8.2.3 Was the Red Algal Acquisition a Unique Event in the History of Evolution? -- 8.2.4 Chromera velia, a (No Longer) Missing Link -- 8.3 Apicoplast Biogenesis -- 8.3.1 Import of Nuclear-encoded Proteins to various Apicoplast Destinations -- 8.3.2 Targeting Signals -- 8.3.3 Crossing the Borders -- 8.3.3.1 The Two Innermost Membranes. , 8.3.3.2 The Second Outermost Membrane -- 8.3.3.3 The Outermost Membrane -- 8.3.4 Organelle Replication and Division-Drug Targets Beyond Metabolism -- 8.3.4.1 Apicoplast Genome Replication and Gene Translation -- 8.3.4.2 Division of the Apicoplast Organelle -- 8.4 Metabolic Functions of the Apicoplast -- 8.4.1 The Apicoplast's Function is Anabolic Metabolism -- 8.4.2 Type II Fatty Acid Synthesis (FASII) -- 8.4.3 Heme Biosynthesis -- 8.4.4 Iron-sulfur Clusters and Isoprenoids -- 8.4.5 Transport of Metabolites -- 8.5 Conclusion -- References -- Part III -- Biogenesis of Chloroplast Proteins -- Chapter 9 -- Mechanisms of Chloroplast Protein Import in Plants -- 9.1 Introductory Topics -- 9.1.1 Background -- 9.1.2 Transit Peptides -- 9.1.3 Energetics and Stages of Import -- 9.1.4 Identification of Translocon Components -- 9.2 Translocation Across the Outer Membrane -- 9.2.1 Components of the TOC Complex -- 9.2.2 TOC Components in Arabidopsis thaliana -- 9.2.3 TOC Complexes -- 9.2.4 Cytosolic Factors and Regulators of Chloroplast Protein Import -- 9.3 Translocation Across the Inner Membrane -- 9.3.1 Arrival and Conductance -- 9.3.2 Import Propulsion -- 9.3.3 Redox Regulation -- 9.3.4 Transit Peptide Cleavage -- 9.4 Targeting to the Envelope Membranes -- 9.4.1 Sorting to the Outer Membrane -- 9.4.2 Sorting to the Intermembrane Space and Inner Membrane -- 9.5 Alternative Protein Import Pathways -- 9.5.1 Dual-Targeting -- 9.5.2 Non-canonical Protein Transport -- 9.6 Concluding Remarks -- References -- Chapter 10 -- Protein Routing Processes in the Thylakoid -- 10.1 Overview of Conservative Protein Sorting to the Thylakoid Membrane and Lumen -- 10.2 The Sec and SRP Transport Pathways in Chloroplasts -- 10.2.1 cpSec Transport -- 10.2.2 cpSRP Transport -- 10.2.3 A Second Sec System -- 10.3 The Twin Arginine Transport (Tat) Pathway in Chloroplasts. , 10.3.1 Introduction.