Chloroplast Biogenesis : From Proplastid to Gerontoplast

Foreword xiii Preface xv Colorplates xvii 1. Introduction 1(18) 1.1. PLASTID FORMS, THEIR STRUCTURAL FLEXIBILITY, AND POTENTIAL FOR TRANSFORMATION 1(2) 1.2. CHLOROPLAST BIOGENESIS: INVOLVEMENT OF THREE PLASTID FORMS 3(12) 1.2.1. Organization of the Plastid Genome, Its Genetic Potential, and Chloroplast Biogenesis 4(4) Semiautonomous Character of Plastid 4(1) The Plastid Genes 5(3) 1.2.2. Nuclear Genes, Gene Products, and Chloroplast Biogenesis 8(1) 1.2.3. Basic Features of the Biogenesis and Signaling Systems 9(3) 1.2.4. Thermodynamic Characteristics of Plastid Transformation 12(3) Proplastid to Mature Chloroplast 12(2) Mature Chloroplast 14(1) Chloroplast to Gerontoplast 15(1) 1.3. DESIGN OF THE BOOK AND THE LIMITATIONS 15(4) 1.3.1. The Book 15(1) 1.3.2. The Limitations 16(3) 2. Proplastid to Chloroplast Transformation 19(60) 2.1. DEVELOPMENT OF INTERNAL MEMBRANE STRUCTURES 19(7) 2.1.1. Etioplast, the Experimental Precursor of Chloroplast 19(1) 2.1.2. Proplastid and Etioplast, the Beginners of Chloroplast Biogenesis 20(2) 2.1.3. Organization of Prolameller Body and Prothylakoid 22(1) 2.1.4. NADPH-Protochlorophyllide Oxidoreductase, a Modulator of Transformation of Prolameller Body to Thylakoid 23(3) Chemistry and Molecular Biology of NADPH-Protochlorophyllide Oxidoreductase 24(1) Types of NADPH-Protochlorophyllide Oxidoreductase 24(1) Photoregulation of NADPH-Protochlorophyllide Oxidoreductase 25(1) 2.2. THYLAKOID FORMATION AND PIGMENT ACCUMULATION 26(8) 2.2.1. Coordination between the Two events 26(1) 2.2.2. Chlorophyll Biosynthesis 27(3) Coordinate Action of NADPH Protochlorophyllide Oxidoreductase and Chlorophyll Synthase, the Final Step of Chlorophyll Biosynthesis 27(2) Heterogeneity in Chlorophyll Biosynthetic Pathways 29(1) Significance of the Heterogeneity and Formation of Different Forms of Light Harvesting Complex 30(1) 2.2.3. Carotenoid Biosynthesis 30(4) 2.2.4. The Lipid Framework 34(1) 2.3. BIOGENESIS AND ASSEMBLY OF LIGHT HARVESTING COMPLEX 34(8) 2.3.1. Assembly of Light Harvesting Complex of Photosystem II 35(5) 2.3.2. Assembly of Light Harvesting Complex of Photosystem I 40(2) 2.4. ASSEMBLY OF INDIVIDUAL THYLAKOID COMPLEXES 42(6) 2.4.1. Photosystem II 44(3) 2.4.2. Photosystem I 47(1) 2.4.3. Cytochrome b/f Complex 47(1) 2.4.4. ATP synthase 48(1) 2.5. RUBISCO ASSEMBLY 48(1) 2.6. CHLOROPLAST PROTEIN TARGETING 49(8) 2.6.1. Import Machine 53(1) 2.6.2. Protein Targeting to the Envelope 54(1) 2.6.3. Targeting of Proteins to the Thylakoids 54(2) The ApH Pathway 54(1) The Sec like Pathway 54(1) The SRP like Pathway 55(1) Targeting by Spontaneous Mechanism 56(1) 2.6.4. Protein Targeting within the Organelle 56(1) 2.7. TEMPORAL APPEARANCE OF THYLAKOID COMPLEXES 57(2) 2.8. FACTORS REGULATING GENE EXPRESSION DURING CHLOROPLAST DEVELOPMENT 59(6) 2.8.1. Photoregulation 60(4) Expression of Light Harvesting Complex Genes 61(1) Expression of Rubisco Genes 61(1) Light at Posttranscriptional Level 62(1) Mechanism of Photosignal Transduction and Gene Expression 63(1) 2.8.2. Circadian Rhythm 64(1) 2.8.3. The Developmental Factor 64(1) 2.9. INTERORGANELLAR COMMUNICATION, GENE EXPRESSION, AND CHLOROPLAST DEVELOPMENT 65(7) 2.9.1. Nuclear Factor(s) for Plastid Gene Activity during Development 65(5) Plastid Gene Expression During Early Development and Posttranscriptional Control 68(1) Control of Translation and Assembly of the Complexes 69(1) 2.9.2. Plastid Factor for the Expression of Nuclear Encoded Photosynthetic Genes during Organelle Development 70(2) 2.10. ENVIRONMENTAL MODULATION OF DEVELOPING CHLOROPLAST 72(7) 3. Mature Chloroplast 79(76) 3.1. CHLOROPLAST ENVELOPE 80(2) 3.2. THE LAMELLAE 82(1) 3.3 LIGHT HARVESTING COMPLEXES 82(5) 3.3.1. Structure of the Light Harvesting Complex Protein 83(1) 3.3.2. Excitors Migration in the Light Harvesting Complex 83(2) 3.3.3. Organization of Light Harvesting Complexes in the Photosystems 85(2) 3.4. PHOTOSYSTEMS: COMPOSITION, STRUCTURAL ORGANIZATION, AND PRIMARY PHOTOCHEMISTRY 87(25) 3.4.1. Structural Similarity Among the Reaction Centers of Photosystems 87(3) 3.4.2. Photosystem II 90(13) The Antenna Proteins 90(1) Reaction Center II 91(3) Mn-Cluster 94(2) Mechanism of Oxygen Evolution 96(4) The Extrinsic Proteins 100(1) Cytochrome b559 101(1) Ionic Cofactors 101(2) 3.4.3. Photosystem I 103(5) Organization and Function of the Subunits 103(2) The Antenna System 105(1) The Electron Transport Components 105(3) Searching for Ligands to the Prosthetic Groups in Reaction Center I 108(1) 3.4.4. Plastocyanin 108(2) Protein-Protein Interactions Among Plastocyanin, Cytochrome f, and Photosystem I 108(2) The Dynamics of Reduction of P700+ and Binding of Plastocyanin to Photosystem I 110(1) 3.4.5. Ferredoxin 110(2) 3.4.6. Ferredoxin-NADP+ Reductase 112(1) 3.4.7. Cyclic Electron Flow 112(1) 3.5. CYTOCHROME b/f COMPLEX: THE LINK BETWEEN THE PHOTOSYSTEMS 112(2) 3.5.1. Structure and organization of the Complex 112(2) 3.5.2. Redox Reactions and Electron Flow through the Complex 114(1) 3.5.3. Regulation of the State Transition 114(1) 3.6. ATP SYNTHASE: STRUCTURE AND MECHANISM OF ACTION 114(4) 3.6.1. Structure of the Enzyme Complex 114(1) 3.6.2. Mechanism of the Enzyme Action 115(2) 3.6.3. Regulation of the Enzyme Activity 117(1) 3.6.4. Energetics of ATP synthesis 117(1) 3.6.5. The Dynamics of ATP Synthesis 118(1) 3.7. THE CALVIN-BENSON CYCLE 118(9) 3.7.1. The Catalytic site 119(2) 3.7.2. Rubisco Activase 121(1) 3.7.3. Energetics of the Cycle 121(1) 3.7.4. Regulation of Carbon Dioxide Fixation 122(1) Light 122(1) Thioredoxin 122(1) 3.7.5. Endogenous Carbon Dioxide Generators and Regulation of Carbon Dioxide Pool 122(5) Photorespiration 122(2) The C4 Path 124(2) Crassulacean Acid Metabolism 126(1) 3.8. OTHER METABOLIC PROCESSES IN MATURE CHLOROPLAST 127(1) 3.8.1. Starch Synthesis 127(1) 3.8.2. Fatty Acid Synthesis 127(1) 3.8.3. Amino Acid Synthesis 127(1) 3.9. CHLOROPLAST UNDER STRESS 128(27) 3.9.1. Chloroplast. the Sensor of Stress in Green Plants 128(2) 3.9.2. Alterations in the Structure and Function of the Photosynthetic Apparatus Induced by stress 130(1) 3.9.3. Stress Targets and Signal Transduction Pathways Associated with Photosystem II 131(3) 3.9.4. Major Adaptive Response of Photosystem II to Stress 134(9) Release of Cat+ and Inactivation of Oxygen Evolving Complex 134(1) Energy Spillover 134(1) Xanthophyll Cycle 135(7) Turnover of Reaction Center II Proteins 142(1) 3.9.5. Photoinhibition of Photosystem I 143(2) 3.9.6. Gene Activity and Stress Adaptation 145(10) Stress Signals and Expression of the Photosynthetic genes 145(4) The Stress Specific Genes 149(3) Oxidative Stress 152(3) 4. Transformation of Chloroplast to Gerontoplast 155(88) 4.1. INTRODUCTION 155(6) 4.1.1. Gerontoplast Is Not a Dead Plastid and Can Be Converted Back to Chloroplast 159(1) 4.1.2. Senescing Leaves Remain Viable during Formation and Activity of Gerontoplasts 160(1) 4.1.3. Physiology of Gerontoplasts 160(1) 4.2. SENESCENCE INDUCED DEGRADATION OF THYLAKOID PROTEINS, LOSS OF PIGMENTS, AND ULTRASTRUCTURAL CHANGES OF MEMBRANES 161(29) 4.2.1. Coordinate Degradation of Membrane Components 161(2) 4.2.2. Protein Loss 162 Senescing Leaves Lose Chloroplast Proteins 163(3) Plastid Located Proteolytic Systems 164(2) Possible Participation of Cytoplasmic Proteases 166(1) 4.2.3. Degradation of Chlorophylls and Its Mechanism 166(8) Chlorophyllase 169(3) Mg-dechelatase 172(1) Pheophorbide a oxygenase 172(2) 4.2.4. Degradation of Carotenoids 174(4) Quantitative Loss and Changes in Composition 174(1) Change in Distribution: From Thylakoid to Plastoglobuli 175(2) Possible Participation of Enzymes in the Pigment Catabolism 177(1) 4.2.5. Lipid Breakdown 178(1) 4.2.6. Leaf Senescence Is Accompanied by Extensive Modification in the Structure and Organization of Chloroplast Membranes 178(12) Ultrastructural Modifications 178(9) Membrane Phase Changes 187(1) Changes in Optical Property 188(2) 4.3. SENESCENCE INDUCED CHANGES IN ELECTRON TRANSPORT COMPLEXES AND RUBISCO 190(16) 4.3.1. Disorganization of Photosystem II 192(6) 4.3.2. Decline in Photosystem l Efficiency 198(2) 4.3.3. Dismantling of Cytochrome b/f Complex and Other Components of Interphotosystem Electron Transport Chain 200(1) 4.3.4. Decline in Photophosphorylation 200(2) 4.3.5. Changes in Rubisco 202(4) Loss in the Activity of Enzyme 202(1) Enzyme Turnover 203(1) Proteolytic Degradation 204(1) Significance of Early and Rapid Loss in the Activity of Enzyme 205(1) 4.4. CHLOROPLAST TO GERONTOPLAST TRANSFORMATION IS ACCOMPANIED BY THE CHANGES IN THE PATTERN OF GENE EXPRESSION IN LEAVES 206(18) 4.4.1. Identification of the Senescence Associated Genes 208(5) 4.4.2. All Senescence Associated Genes May Not Be Senescence Specific 213(7) 4.4.3. Senescence Associated Genes for Macromolecular Degradation and Mobilization 220(4) Mobilization of Nitrogen 220(2) Conversion of Lipids, Polysaccharides, and Amino Acids to Respiratory Substrates 222(1) Storage and Mobilization of Mineral Nutrients 223(1) Gene Expression against Free Radical Induced Damage 223(1) Pathogenesis Related Genes 224(1) 4.5. SENESCENCE SIGNALS AND OTHER REGULATING FACTORS 224(16) 4.5.1. The Signals for Expression of Senescence Associated Genes 225(6) Hormones 225(3) Age Dependent Photosynthetic Signal 228(1) Signal from Developing Sink 229(1) Stress Signal 229(2) 4.5.2. Intracellular Factors and Signaling 231(3) Nuclear Factor 232(1) Plastid Factor 232(2) Plastid Specific Redox Signals 234(1) 4.5.3. The Cell Type Signals 234(1) 4.5.4. Environmental Signaling and Regulation: Photoregulation 235(5) Light May Regulate through Photosynthesis 235(1) Action of Light through Phytochrome 236(2) Light Signal and Regulation of Leaf Senescence under Canopy 238(2) 4.6. STRESS RESPONSE OF THE SENESCING LEAVES AND MODIFICATIONS OF GERONTOPLAST 240(3) 5. Conclusion and the Future 243(8) 5.1. THE PICTURE OF MECHANISMS OF ASSEMBLY OF CHLOROPLAST COMPLEXES DURING DEVELOPMENT AND THEIR DEMOLITION DURING SENESCENCE IS HAZY 244(1) 5.2. THE MECHANISMS OF DEGRADATION OF PROTEIN AND CHLOROPHYLL DURING BIOGENESIS OF THE ORGANELLE LARGELY REMAIN UNCLEAR 245(1) 5.3. MOLECULAR BIOLOGY OF GERONTOPLAST FORMATION DURING LEAF SENESCENCE, A CHALLANGING AREA OF RESEARCH FOR FUTURE 246(1) 5.4. THE SIGNALING SYSTEMS ASSOCIATED WITH TRANSFORMATIONS OF PROPLASTID TO CHLOROPLAST AND CHLOROPLAST TO GERONTOPLAST ARE POORLY UNDESTOOD 247(2) 5.5. ENVIRONMENTAL MODULATION OF CHLOROPLAST BIOGENESIS IS LESS KNOWN 249(1) 5.6. THE STUDY OF CHLOROPLAST BIOGENESIS NEEDS BETTER LABORATORY MODELS 249(2) References 251(86) Abbreviations 337(8) Index 345