Editorial ....................................................................... v Contents ...................................................................... vii Preface ...................................................................... xvii Color Plates ................................................................. CP-1 Part I: Evolution, Complexity and Regulation of Photosynthetic Structures 1 Thylakoid Biogenesis and Dynamics: The Result of a Complex Phylogenetic Puzzle Reinhold. G. Herrmann and Peter Westhoff Summary ................................................................. 1 I. Introduction ....................................................... 2 II. Aspects of Chloroplast and Plant Genome Evolution-Plant Genome Structure .......................................................... 5 III. Functional Consequences of Genome Rearrangement-Regulatory Levels ............................................................ 11 IV. The Impact of Multicellularity and Terrestrial Life upon Thylakoid Biogenesis .............................................. 18 V. Maintenance and Acclimation of Thylakoids ......................... 19 VI. Outlook-New Approaches ............................................ 21 Acknowledgments ........................................................ 23 References ............................................................. 23 Part II: Gene Expression and Signal Transduction 2 Plastid RNA Polymerases in Higher Plants Karsten Liere and Pal Maliga Summary ................................................................ 29 I. Introduction ...................................................... 30 II. The Plastid-Encoded Plastid RNA Polymerase (PEP) .................. 31 III. The Nuclear-Encoded Plastid RNA Polymerase (NEP) .................. 39 IV. The Role of NEP and PEP in Plastid Gene Expression ................ 43 V. Unsolved Mystery: tRNA Transcription .............................. 43 Acknowledgments ........................................................ 44 References ............................................................. 44 3 Phytochrome and Regulation Of Photosynthetic Gene Expression Michael Malakhov and Chris Bowler Summary ................................................................ 51 I. Introduction ...................................................... 52 II. Activation of Phytochrome and Other Photoreceptors ................ 52 III. Second Messengers in Phytochrome Signal Transduction .............. 53 IV. Genetic Approaches to Dissect Phytochrome Signaling ............... 54 V. Nuclear-Localized Components of the Light Signaling Machinery ..... 57 VI. Interactions Between Phytochrome and Other Signaling Pathways ..... 61 VII. Concluding Remarks ................................................ 62 Acknowledgments ........................................................ 62 References ............................................................. 63 4 Regulating Synthesis of the Purple Bacterial Photosystem Carl E. Bauer Summary ................................................................ 67 I. Introduction ...................................................... 68 II. The Purple Bacterial Photosystem .................................. 68 III. The Photosynthesis Gene Cluster ................................... 69 IV. Regulating Photosystem Synthesis .................................. 70 V. Concluding Statements ............................................. 79 Acknowledgment ......................................................... 79 References ............................................................. 79 5 Redox Regulation of Photosynthetic Genes Gerhard Link Summary ................................................................ 85 I. Introduction ...................................................... 86 II. Redox Regulation of Nuclear Genes for Photosynthetic Proteins ..... 89 III. Redox Regulation of Gene Expression Inside the Chloroplast ........ 93 IV. Outlook ........................................................... 100 Acknowledgments ....................................................... 102 References ............................................................ 102 6 Sugar Sensing and Regulation of Photosynthetic Carbon Metabolism Uwe Sonnewald Summary ............................................................... 109 I. Photosynthetic Carbon Metabolism in C3 Plants .................... 110 II. Sink Regulation of Photosynthesis ................................ 112 III. Sugar Regulation of Gene Expression .............................. 114 Acknowledgment ........................................................ 118 References ............................................................ 118 7 Editing, Polyadenylation and Degradation of mRNA in the Chloroplast Gadi Schuster and Ralph Bock Summary ............................................................... 121 I. Introduction ..................................................... 122 II. RNA Editing in the Chloroplast ................................... 122 III. Polyadenylation and Degradation of mRNA in the Chloroplast ....... 126 Acknowledgments ....................................................... 132 References ............................................................ 133 8 Regulation of Chloroplast Translation Aravind Somanchi and Stephen P. Mayfield Summary ............................................................... 137 I. Introduction ..................................................... 138 II. Translation in the Chloroplast-An Overview ....................... 138 III. Translational Regulation in the Chloroplast ...................... 139 IV. Mechanism of Translational Activation ............................. 145 V. Conclusions and Perspectives ...................................... 147 References ............................................................ 148 Part III: Biogenesis, Turnover and Senescence 9 Proteins Involved in Biogenesis of theThylakoid Membrane Klaas Jan van Wijk Summary ............................................................... 153 I. Introduction .................................................... 154 II. Chloroplast Proteins Involved in Targeting and Insertion into the Thylakoid Membrane .......................................... 155 III. Peptidases and Proteases Responsible for Processing and Turnover ........................................................ 161 IV. Proteins involved in Folding and Post-translational Modifications ................................................... 162 V. Proteins Assisting in Protein and Cofactor Transport, Storage and Ligation .................................................... 163 VI. Vesicles Formation, Low Density Membranes and Tubules ........... 167 VII. Proteomics as a Tool for Identification of Proteins involved in Thylakoid Biogenesis ......................................... 168 VIII. Conclusions and Perspectives .................................... 169 Acknowledgments ....................................................... 170 References ............................................................ 170 10 Peptidyl-Prolyl Isomerases and Regulation of Photosynthetic Functions Alexander V. Vener Summary ............................................................... 177 I. Introduction ..................................................... 178 II. Structure and Function of Peptidyl-Prolyl Isomerases (PPIases) ... 179 III. Plant PPIases .................................................... 184 IV. PPIases and Photosynthetic Function .............................. 187 References ............................................................ 190 11 Role of the Plastid Envelope in the Biogenesis of Chloroplast Lipids Maryse A. Block, Eric Marechal and Jacques Joyard Summary ................................................................ 195 I. Introduction .................................................... 196 II. Lipid Composition of Chloroplast Membranes ...................... 197 III. Biosynthesis of Chloroplast Glycerolipids ....................... 200 IV. Chlorophyll Biosynthesis ........................................ 208 V. Plastid Prenylquinone Biosynthesis .............................. 209 VI. Transport of Lipids From ER to Chloroplasts and Between Chloroplast Membranes ........................................... 210 VII. Lipid Modifications of Proteins in Chloroplasts ................. 211 VIII. Conclusion ...................................................... 213 Acknowledgment ........................................................ 214 References ............................................................ 214 12 Pigment Assembly - Transport and Ligation Harald Paulsen Summary ............................................................... 219 I. Introduction ..................................................... 220 II. Assembly of Chlorophyll a/b-Protein Complexes .................... 220 III. Assembly of Chlorophyll a-Protein Complexes ...................... 222 IV. How are Pigments Synthesized and Transported? .................... 223 V. How Do Pigments Find Their Correct Binding Site? ................. 225 VI. Are Pigments Involved in the Assembly of Multi-protein Complexes of the Photosynthetic Apparatus? ....................... 228 Acknowledgments ....................................................... 230 References ............................................................ 230 13 Chlorophyll Biosynthesis - Metabolism and Strategies of Higher Plants to Avoid Photooxidative Stress Klaus Apel Summary ............................................................... 235 I. Introduction ..................................................... 236 II. Tetrapyrrole Biosynthesis and Photooxidative Stress .............. 236 III. Regulatory Steps in Tetrapyrrole Biosynthesis .................... 239 IV. Tetrapyrrole Derivatives as Plastid Signals ....................... 247 V. Outlook ........................................................... 249 Acknowledgments ....................................................... 249 References ............................................................ 249 14 Transport of Metals: A Key Process in Oxygenic Photosynthesis Himadri Pakrasi, Teruo Ogawa and Maitrayee Bhattacharrya-Pakrasi Summary ............................................................... 253 I. Introduction .................................................... 254 II. Different Classes of Transporters ............................... 254 III. Iron ............................................................ 257 IV. Copper .......................................................... 258 V. Manganese ....................................................... 259 VI. Zinc ............................................................ 260 VII. Magnesium ....................................................... 261 VIII. Concluding Remarks .............................................. 262 Acknowledgments ....................................................... 262 References ............................................................ 262 15 Chloroplast Proteases and Their Role in Photosynthesis Regulation Zach Adam Summary ............................................................... 265 I. Introduction ..................................................... 266 II. Substrates for Proteolysis ....................................... 266 III. Proteolytic Enzymes .............................................. 268 IV. Conclusions and Future Prospects ................................. 271 Acknowledgments ....................................................... 273 References ............................................................ 273 16 Senescence and Cell Death in Plant Development: Chloroplast Senescence and its Regulation Philippe Matile Summary ............................................................... 277 I. Introduction ..................................................... 278 II. Leaf Senescence .................................................. 278 III. Biochemistry of Breakdown in Senescing Chloroplasts .............. 281 IV. Programmed Cell Death ............................................ 287 V. Outlook .......................................................... 290 References ............................................................ 291 Part IV: Regulation of Carbon Metabolism 17 Dynamics of Photosynthetic C02 Fixation: Control, Regulation and Productivity Steven Gutteridge and Douglas B. Jordan Summary ............................................................... 297 I. Crop Yields, Land Use and Population Growth ...................... 298 II. Photosynthesis-Light, Capture, Action ............................ 298 III. Modulating Rubisco Activity and the Response of Photosynthetic CO2-fixation in planta ........................................... 303 IV. Modulating Activities of Other Enzymes of the PCR Cycle .......... 305 V. C4 Metabolism .................................................... 307 VI. Concluding Remarks ............................................... 309 Acknowledgment ........................................................ 310 References ............................................................ 310 18 Chloroplastic Carbonic Anhydrases Goran Samuelsson and Jan Karlsson Summary ............................................................... 313 I. Introduction ..................................................... 314 II. Gene Families .................................................... 314 III. Structure ........................................................ 315 IV. Inhibitors ....................................................... 316 V. Carbonic anhydrase catalysed functions in Chloroplasts ........... 316 References ............................................................ 319 19 Thioredoxin and Glutaredoxin: General Aspects and Involvement in Redox Regulation Arne Holmgren Summary ............................................................... 321 I. Introduction ..................................................... 322 II. Thioredoxins ..................................................... 322 III. Thioredoxin Reductases ........................................... 325 IV. Glutaredoxins .................................................... 326 Acknowledgments ....................................................... 329 References ............................................................ 329 20 The Structure and Function of the Ferredoxin / Thioredoxin System in Photosynthesis Peter Schurmann and Bob B. Buchanan Summary ............................................................... 332 I. Introduction .................................................... 332 II. Biochemical Setting for Thioredoxin-Linked Regulation ........... 333 III. Thioredoxin Regulated Processes ................................. 333 IV. Structure and Function of the Proteins in the Regulatory Chain ........................................................... 334 V. Target Enzymes .................................................. 343 VI. Mechanism for Reduction of Thioredoxins and Target Enzymes ...... 350 VII. Phylogenetic History of Thioredoxins and Photosynthetic Target Enzymes ......................................................... 353 VIII. Concluding Remarks .............................................. 353 Acknowledgments ....................................................... 355 References ............................................................ 355 21 Reversible Phosphorylation in the Regulation of Photosynthetic Phosphoenolpyruvate Carboxylase in C4 Plants Jean Vidal, Sylvie Coursol, Jean-Noel Pierre Summary ............................................................... 363 I. Introduction ..................................................... 364 II. C4 Phosphoenolpyruvate Carboxylase (PEPC) in the Physiological Context of C4 Photosynthesis ..................................... 364 III. Properties of C4 PEPC ............................................ 364 IV. C4 PEPC Activity is Reversibly Modulated in vivo by a Regulatory Phosphorylation Cycle ............................... 366 V. Significance of the Regulatory Phosphorylation of C4 PEPC ........ 370 VI. Conclusions and Perspectives ..................................... 373 References ............................................................ 373 Part V: Acclimation and Stress Responses 22 Photodamage and D1 Protein Turnover in Photosystem II Bertil Andersson and Eva-Mari Aro Summary ............................................................... 377 I. Introduction ..................................................... 378 II. Light-induced Inactivation and Damage to the Photosystem II Reaction Center .................................................. 378 III. Proteolysis of the Damaged D1 Protein ............................ 381 IV. Location of Photosystem II Damage and Repair in the Thylakoid Membrane ........................................................ 385 V. Biogenesis and Assembly of the New D1 Copy into Photosystem II ... 386 Acknowledgments ....................................................... 390 References ............................................................ 390 23 Phosphorylation of Photosystem II Proteins Eevi Rintamaki and Eva-Mari Aro Summary ............................................................... 395 I. Introduction ..................................................... 396 II. Thylakoid Phosphoproteins ........................................ 396 III. Reversible Phosphorylation of Thylakoid Proteins ................. 398 IV. Photosystem II and Light-Harvesting Complex II Protein Phosphorylation in Taxonomically Divergent Oxygenic Photosynthetic Organisms ......................................... 406 V. Physiological Role of Thylakoid Protein Phosphorylation .......... 407 VI. Future Perspective: Is Thylakoid Protein Phosphorylation Involved in the Relay of Signals for Acclimation Processes? ...... 411 Acknowledgments ....................................................... 412 References ............................................................ 412 24 Novel Aspects on the Regulation of Thylakoid Protein Phosphorylation Itzhak Ohad, Martin Vink, Hagit Zer, Reinhold G. Herrmann and Bertil Andersson Summary ............................................................... 419 I. Introduction ..................................................... 420 II. Redox Control of Thylakoid Protein Phosphorylation ............... 420 III. Role of Thiol Redox State in Kinase Activation / Deactivation Process in Isolated Thylakoids ................................... 424 IV. Light-Induced Modulation of Thylakoid Protein Phosphorylation at the Substrate Level ........................................... 425 V. Thylakoid Protein Dephosphorylation and its Regulation ........... 427 VI. Thylakoid Protein Phosphorylation and State Transition: Open Questions ................................................... 427 Acknowledgments ....................................................... 429 References ............................................................ 429 25 Enzymes and Mechanisms for Violaxanthin-Zeaxanthin Conversion Marie Eskling, Anna Emanuelsson and Hans-Erik Akerlund Summary ............................................................... 433 I. Introduction ..................................................... 434 II. The Xanthophyll Cycle, Enzymes and Pigments ...................... 434 III. The Conversion of Violaxanthin Depends on Temperature and Light ........................................................ 441 IV. The Role of the Xanthophyll Cycle ................................ 442 Acknowledgments ....................................................... 447 References ............................................................ 447 26 The PsbS Protein: A Cab-Protein with a Function of Its Own Christiane Funk Summary ............................................................... 453 I. Introduction ..................................................... 454 II. Early History of the PsbS Protein: A Mysterious Protein in Photosystem II ................................................ 456 III. The psbS Gene and Gene Product ................................... 457 IV. Pigment Binding .................................................. 458 V. The PsbS Protein: An Early Ligh Induced Protein or Light Harvesting Protein or a Protein of Its Own? ...................... 459 VI. The Function of the PsbS Protein ................................. 463 VII. Conclusion ....................................................... 464 Acknowledgments ....................................................... 465 References ............................................................ 465 27 Redox Sensing of Photooxidative Stress and Acclimatory Mechanisms in Plants Stanislaw Karpinski, Gunnar Wingsle, Barbara Karpinska and Jan-Erik Hallgren Summary ............................................................... 469 I. Introduction ..................................................... 470 II. Stress and Acclimation ........................................... 470 III. Concluding Remarks ............................................... 482 Acknowledgments ....................................................... 482 References ............................................................ 482 28 The Elip Family of Stress Proteins in theThylakoid Membranes of Pro- and Eukaryota Iwona Adamska Summary ............................................................... 487 I. Introduction .................................................... 488 II. What is an Elip? Past and Present Definitions ................... 488 III. Division of Elip Family Based on Predicted Protein Structure .... 490 IV. Genomic Organization of Elip Family in Arabidopsis thaliana...... 495 V. Similarities and Differences Between the Elip and Cab Gene Families ........................................................ 495 VI. Are Elips Chlorophyll-Binding Proteins? ......................... 500 VII. Possible Physiological Functions of Elip Family Members ......... 500 VIII. Evolutionary Aspects ............................................ 502 IX. Concluding Remarks .............................................. 502 Acknowledgments ....................................................... 502 References ............................................................ 503 29 Regulation, Inhibition and Protection of Photosystem I Yukako Hihara and Kintake Sonoike Summary ............................................................... 508 I. Introduction ..................................................... 508 II. Regulation of the Quantity of PS I ............................... 509 III. Regulation of the Activity of PS I ............................... 513 IV. Regulation of PS I Expression .................................... 513 V. Inhibition of PS I by Environmental Factors ...................... 519 VI. Protection of Photosystem I from Photoinhibition ................. 521 VII. Concluding Remarks ............................................... 524 Acknowledgments ....................................................... 525 References ............................................................ 525 30 Regulation of Photosynthetic Electron Transport Peter J. Nixon and Conrad W. Mullineaux Summary ............................................................... 534 I. Introduction .................................................... 534 II. Background Concepts ............................................. 535 III. Feedback Control of the Photosynthetic Electron Transport Chain ........................................................... 537 IV. Regulation of Photosystem II Activity-The Bicarbonate Effect .... 540 V. Cyclic Electron Flow ............................................ 541 VI. Chlororespiration and Cyanobacterial Respiration ................ 547 VII. Interaction between Chloroplasts and Mitochondria ............... 548 VIII. Questions for the Future ........................................ 549 References ............................................................ 550 Part VI: Photosynthetic Regulation and Genomics - Methodological Implications for the Future 31 Functional Genomics in Synechocystis sp. PCC6803: Resources for Comprehensive Studies of Gene Function and Regulation Takakazu Kaneko and Satoshi Tabata Summary ............................................................... 557 I. Introduction ..................................................... 557 II. CyanoBase and CyanoMutants-Genome Information Databases .......... 558 III. Genome-wide Monitoring of Gene Expression by Proteome and Transcriptome Analyses ........................................... 559 References ............................................................ 561 32 Arabidopsis Genetics and Functional Genomics in the Post - Genome Era Wolf-Rudiger Scheible, Todd A. Richmond, lain W. Wilson and Chris R. Somerville Summary ............................................................... 563 I. Introduction ..................................................... 564 II. Arabidopsis Expressed Sequence Tags and Genome Sequencing Projects ......................................................... 565 III. Classical Arabidopsis Genetics in the Post-Genome Era ............ 571 IV. Assigning Gene Functions Using the Tools of Functional Genomics ......................................................... 575 V. Reverse Arabidopsis Genetics ..................................... 582 VI. Conclusions and Outlook .......................................... 585 Acknowledgments ....................................................... 585 References ............................................................ 585 Index ......................................................................... 593