Chlamydomonas Sourcebook: Organellar and Metabolic Processes (eBook)

Front Cover 1
The Chlamydomonas Sourcebook 4
Copyright Page 5
Contents of Volume 2 6
Preface 16
Acknowledgments 20
List of Contributors 22
Conventions Used 26
Abbreviations 28
List of Tables 32
List of Figures 36
Contents of Volume 1 42
Contents of Volume 3 44
CHAPTER 1 Starch Metabolism 50
I. Starch structure and localization in the green algae 51
II. An outline of the starch metabolism pathway: comparative biochemistry and genomics 54
III. The genetics of starch accumulation and mobilization 67
IV. Physiology of starch storage: circadian clock control, pyrenoidal starch synthesis and hydrogen production 75
V. Conclusions 79
References 82
CHAPTER 2 Glycerolipid Biosynthesis 90
I. Introduction 90
II. Fatty acid biosynthesis and desaturation 93
III. Glycerolipid biosynthesis 98
IV. Compartmentalization of lipid biosynthesis 108
V. Perspectives 109
Acknowledgments 109
References 110
CHAPTER 3 Nitrogen Assimilation and its Regulation 118
I. Introduction 119
II. Useful nitrogen sources for Chlamydomonas 119
III. Ammonium assimilation 130
IV. Assimilation of nitrate and nitrite 134
V. Regulation of nitrate assimilation 146
Acknowledgments 148
References 149
CHAPTER 4 Amino Acid Metabolism 164
I. Introduction 165
II. Biosynthesis of amino acids: pathways, enzymes, localization, inhibitors, mutants 165
III. Use of exogenous amino acids 191
IV. Role of amino acids as precursor of metabolites 195
V. Conclusion 199
References 199
CHAPTER 5 Sulfur: From Acquisition to Assimilation 208
I. Introduction 208
II. SO[sup(2–)][sub(4)] acquisition and assimilation 209
III. S starvation responses 220
IV. Perspectives 227
Acknowledgments 228
References 228
CHAPTER 6 Phosphate Metabolism and Responses to Phosphorus Deficiency 238
I. Introduction 239
II. Phosphorus acquisition 241
III. P storage, mobilization, and conservation 244
IV. Genetic control of phosphorus deprivation responses 247
V. P deficiency and photosynthesis 254
VI. Regulatory model for P deprivation responses 256
VII. Concluding remarks 257
Acknowledgments 258
References 258
CHAPTER 7 Hydrogenases, Hydrogen Production, and Anoxia 266
I. Background 267
II. Hydrogenases 269
III. Hydrogen metabolism 278
IV. Fermentative metabolism 285
V. Genomics and systems biology 288
VI. Sulfur deprivation 290
VII. Outlook 294
Acknowledgments 295
References 295
CHAPTER 8 The CO[sub(2)]-Concentrating Mechanism and Carbon Assimilation 306
I. The carbon environment 306
II. Metabolism of carbon assimilation 318
III. Acquisition of inorganic carbon 327
References 339
CHAPTER 9 Rubisco 352
I. Introduction 352
II. Rubisco-encoding genes and enzyme structure 353
III. Site-directed mutagenesis 355
IV. Rubisco activase 369
V. Rubisco expression in response to physiological cues 370
VI. Regulation of Rubisco LS expression 372
VII. Conclusions and perspectives 373
Acknowledgements 374
References 374
CHAPTER 10 Transition Metal Nutrition: A Balance Between Deficiency and Toxicity 382
I. Introduction 383
II. Components of the metal homeostasis network 384
III. Metal tolerance 403
IV. Metal nutrition and deficiency response 408
V. Conclusions and perspectives 425
Acknowledgments 428
References 428
CHAPTER 11 Thioredoxins and Related Proteins 450
I. Introduction 450
II. Thioredoxins 452
III. Glutaredoxins 470
IV. Protein disulfide isomerases 476
V. Conclusion 479
Acknowledgments 480
References 481
CHAPTER 12 The Mitochondrial Genome 494
I. Introduction 495
II. Characteristics of the mitochondrial genome 496
III. Mutations affecting the mitochondrial genome 499
IV. Mitochondrial genome transmission 506
V. Mitochondrial transformation 509
Acknowledgments 510
References 510
CHAPTER 13 Oxidative Phosphorylation: Building Blocks and Related Components 518
I. Introduction 519
II. Complexes of the mitochondrial respiratory chain 520
III. Import of nucleus-encoded OXPHOS proteins 536
IV. Conclusions and perspectives 539
Acknowledgments 540
References 540
CHAPTER 14 Light-Harvesting Proteins 552
I. Introduction 553
II. Structure and composition of the light-harvesting apparatus 554
III. Light-harvesting proteins 562
IV. LHC-like proteins 570
V. Regulation of the light-harvesting complex 574
Acknowledgments 577
References 578
CHAPTER 15 Photosystem I 590
I. Introduction 591
II. Composition of PS I 594
III. Energy transfer and electron transfer within PS I 597
IV. Electron transfer to and from PS I 608
V. Assembly and disassembly of PS I 613
VI. Frontiers of PS I research using the Chlamydomonas system 614
Acknowledgments 614
References 614
CHAPTER 16 Photosystem II, a Structural Perspective 622
I. Introduction 622
II. Overview of the photosystem II complex 623
III. Beyond the photosystem II crystal structure 643
References 643
CHAPTER 17 The Cytochrome b[sub(6)]f Complex 652
I. Introduction 653
II. Structure of the b[sub(6)]f complex 653
III. The b[sub(6)]f complex at the crossroads of electron transport and signal transduction 660
IV. Biogenesis of the b[sub(6)]f complex 668
V. Conclusion 676
Acknowledgments 677
References 677
CHAPTER 18 The CF[sub(0)]F[sub(1)] ATP Synthase Complex of Photosynthesis 688
I. Introduction 689
II. Composition, structure and specific features of the ATP synthase 689
III. Mechanistic aspects of the synthesis/hydrolysis of ATP 698
IV. Concluding remarks 710
References 711
CHAPTER 19 Chaperones and Proteases 720
I. Introduction 721
II. Regulation of the heat shock response 722
III. Small HSPs 723
IV. HSP33: a redox-regulated chaperone 725
V. HSP60s 726
VI. HSP70s 727
VII. HSP90s 741
VIII. Elevated levels of sHSPs, HSP60, and HSP70 in Chlamydomonas acidophila 744
IX. HSP100 proteins function as chaperones and/or components of ATP-dependent proteases 744
X. FtsH proteases 748
XI. Lon 749
XII. DegP and C-terminal processing peptidases 749
XIII. N-terminal maturation of organelle-encoded proteins 752
XIV. Peptidases in organellar import and membrane translocation 753
XV. Intramembrane proteases: Site2 peptidase, PARL/rhomboid, Spp, SppA 755
XVI. Proteolytic processes in the organelles of Chlamydomonas: whodunnit? 758
XVII. Conclusion 761
References 761
CHAPTER 20 Biosynthesis of Chlorophylls and Hemes 780
I. Introduction 781
II. Outline of tetrapyrrole biosynthesis 782
III. ALA formation from glutamate 782
IV. Steps common to the biosynthesis of all tetrapyrroles 791
V. Steps from uroporphyrinogen III to protoporphyrin IX 794
VI. Steps specific to chlorophyll formation 797
VII. Biosynthesis of chlorophyll b 809
VIII. Minor chlorophyll a derivatives in reaction centers 810
IX. Chlorophyll degradation and interconversion of chlorophylls a and b 810
X. The branch from uroporphyrinogen III to siroheme 812
XI. The branch from protoporphyrin IX to hemes 814
XII. Heme catabolism 818
XIII. Regulation 819
References 824
CHAPTER 21 Carotenoids 848
I. Introduction 848
II. Occurrence and analysis 849
III. Biosynthesis 852
IV. Localization and functional significance 857
V. Carotenoids as biosynthetic precursors 859
VI. Outlook 859
Acknowledgments 860
References 860
CHAPTER 22 State Transitions 868
I. Introduction 869
II. What are state transitions? 869
III. Phosphorylation and mobility of LHCII polypeptides 871
IV. Regulation of phosphorylation 877
V. Thylakoid protein kinases 879
VI. Maintenance of ATP levels through state transitions 885
VII. Genetic approaches 886
VIII. Role of state transitions 888
IX. Conclusions and prospects 888
Acknowledgments 889
References 889
CHAPTER 23 Photoprotection and High Light Responses 896
I. Introduction 896
II. High light-induced damage and repair 898
III. Regulation of photosynthetic light harvesting by nonphotochemical quenching 902
IV. Regulation of gene expression and acclimation to high light 905
Acknowledgments 910
References 911
CHAPTER 24 The Chloroplast Genome 920
I. Introduction 920
II. Genome structure and sequence 921
III. Gene content 927
IV. DNA replication 929
V. Genome evolution 931
VI. Conclusions and perspectives 934
References 935
CHAPTER 25 Chloroplast Transcription 942
I. Introduction 942
II. Transcription units: single genes and gene clusters 943
III. The transcription machinery 944
IV. Initiation and termination of transcription 951
V. Regulation of chloroplast transcription 956
VI. Perspectives 958
Acknowledgments 958
References 958
CHAPTER 26 Chloroplast RNA Splicing 964
I. Introduction 964
II. Group I Introns 965
III. Group II intron splicing 970
IV. Are splicing and its regulation essential? 977
V. Conclusions 978
Acknowledgments 979
References 979
CHAPTER 27 Chloroplast RNA Processing and Stability 986
I. Chloroplast RNA processing 987
II. Chloroplast RNA stability and degradation 998
III. Conclusions and perspectives 1007
Acknowledgments 1008
References 1008
CHAPTER 28 Protein Synthesis in the Chloroplast 1016
I. Introduction 1017
II. Methodologies used in studies of chloroplast translation 1018
III. Chloroplast ribosomes 1020
IV. General chloroplast translation factors 1033
V. The regulation of translation by light 1037
VI. Genetic approaches that have identified chloroplast translation factors 1044
VII. Cis-acting translation elements in chloroplast 5' UTRs 1049
VIII. mRNA termini may interact during translation 1054
IX. The localization of protein synthesis 1055
X. Translation and protein targeting 1057
XI. Future perspectives 1057
Acknowledgments 1058
References 1058
CHAPTER 29 The CES Process 1076
I. Introduction 1077
II. Assembly of multisubunit photosynthetic protein complexes 1078
III. CES, a major control step in the biogenesis of photosynthetic proteins 1082
IV. CES cascades and assembly of multimeric protein complexes 1089
V. Is CES central to organelle protein expression? 1093
VI. CES and the nuclear control of chloroplast gene expression 1098
VII. Conclusion 1102
Acknowledgments 1102
References 1102
Index 1114
A 1114
B 1115
C 1115
D 1116
E 1116
F 1116
G 1116
H 1117
I 1117
J 1117
K 1117
L 1117
M 1117
N 1118
O 1118
P 1118
Q 1119
R 1119
S 1119
T 1120
U 1120
V 1120
W 1120
X 1120
Y 1120
Z 1120