Stern The Chlamydomonas Sourcebook: Organellar and Metabolic Processes

Volume 2
2. Auflage 2009
ISBN: 978-0-08-091956-0
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 1040 Seiten

This second volume of The Chlamydomonas Sourcebook provides the background and techniques for using this important organism in plant research. From biogenesis of chloroplasts and mitochondria and photosynthesis to respiration and nitrogen assimilation, this volume introduces scientists to the functions of the organism. The volume then moves on to starch biosynthesis, sulfur metabolism, response to heavy metals, and hydrogen production. - Describes molecular techniques, analysis of the recently sequenced genome, and reviews of the current status of the diverse fields in which Chlamydomonas is used as a model organism - Includes contributions from leaders in particular areas of research - Provides methods for Chlamydomonas research and best practices for applications in research, including methods for culture, preservation of cultures, preparation of media, lists of inhibitors and other additives to culture media - Assists researchers with common laboratory problems such as contamination - Includes valuable student demonstrations and properties of particular strains and mutants - Edited by the leading researcher in Chlamydomonas science

Autoren/Hrsg.

Stern, David

Inhaltsverzeichnis

1;Front Cover;1
2;The Chlamydomonas Sourcebook;4
3;Copyright Page;5
4;Contents of Volume 2;6
5;Preface;16
6;Acknowledgments;20
7;List of Contributors;22
8;Conventions Used;26
9;Abbreviations;28
10;List of Tables;32
11;List of Figures;36
12;Contents of Volume 1;42
13;Contents of Volume 3;44
14;CHAPTER 1 Starch Metabolism;50
14.1;I. Starch structure and localization in the green algae;51
14.2;II. An outline of the starch metabolism pathway: comparative biochemistry and genomics;54
14.3;III. The genetics of starch accumulation and mobilization;67
14.4;IV. Physiology of starch storage: circadian clock control, pyrenoidal starch synthesis and hydrogen production;75
14.5;V. Conclusions;79
14.6;References;82
15;CHAPTER 2 Glycerolipid Biosynthesis;90
15.1;I. Introduction;90
15.2;II. Fatty acid biosynthesis and desaturation;93
15.3;III. Glycerolipid biosynthesis;98
15.4;IV. Compartmentalization of lipid biosynthesis;108
15.5;V. Perspectives;109
15.6;Acknowledgments;109
15.7;References;110
16;CHAPTER 3 Nitrogen Assimilation and its Regulation;118
16.1;I. Introduction;119
16.2;II. Useful nitrogen sources for Chlamydomonas;119
16.3;III. Ammonium assimilation;130
16.4;IV. Assimilation of nitrate and nitrite;134
16.5;V. Regulation of nitrate assimilation;146
16.6;Acknowledgments;148
16.7;References;149
17;CHAPTER 4 Amino Acid Metabolism;164
17.1;I. Introduction;165
17.2;II. Biosynthesis of amino acids: pathways, enzymes, localization, inhibitors, mutants;165
17.3;III. Use of exogenous amino acids;191
17.4;IV. Role of amino acids as precursor of metabolites;195
17.5;V. Conclusion;199
17.6;References;199
18;CHAPTER 5 Sulfur: From Acquisition to Assimilation;208
18.1;I. Introduction;208
18.2;II. SO[sup(2–)][sub(4)] acquisition and assimilation;209
18.3;III. S starvation responses;220
18.4;IV. Perspectives;227
18.5;Acknowledgments;228
18.6;References;228
19;CHAPTER 6 Phosphate Metabolism and Responses to Phosphorus Deficiency;238
19.1;I. Introduction;239
19.2;II. Phosphorus acquisition;241
19.3;III. P storage, mobilization, and conservation;244
19.4;IV. Genetic control of phosphorus deprivation responses;247
19.5;V. P deficiency and photosynthesis;254
19.6;VI. Regulatory model for P deprivation responses;256
19.7;VII. Concluding remarks;257
19.8;Acknowledgments;258
19.9;References;258
20;CHAPTER 7 Hydrogenases, Hydrogen Production, and Anoxia;266
20.1;I. Background;267
20.2;II. Hydrogenases;269
20.3;III. Hydrogen metabolism;278
20.4;IV. Fermentative metabolism;285
20.5;V. Genomics and systems biology;288
20.6;VI. Sulfur deprivation;290
20.7;VII. Outlook;294
20.8;Acknowledgments;295
20.9;References;295
21;CHAPTER 8 The CO[sub(2)]-Concentrating Mechanism and Carbon Assimilation;306
21.1;I. The carbon environment;306
21.2;II. Metabolism of carbon assimilation;318
21.3;III. Acquisition of inorganic carbon;327
21.4;References;339
22;CHAPTER 9 Rubisco;352
22.1;I. Introduction;352
22.2;II. Rubisco-encoding genes and enzyme structure;353
22.3;III. Site-directed mutagenesis;355
22.4;IV. Rubisco activase;369
22.5;V. Rubisco expression in response to physiological cues;370
22.6;VI. Regulation of Rubisco LS expression;372
22.7;VII. Conclusions and perspectives;373
22.8;Acknowledgements;374
22.9;References;374
23;CHAPTER 10 Transition Metal Nutrition: A Balance Between Deficiency and Toxicity;382
23.1;I. Introduction;383
23.2;II. Components of the metal homeostasis network;384
23.3;III. Metal tolerance;403
23.4;IV. Metal nutrition and deficiency response;408
23.5;V. Conclusions and perspectives;425
23.6;Acknowledgments;428
23.7;References;428
24;CHAPTER 11 Thioredoxins and Related Proteins;450
24.1;I. Introduction;450
24.2;II. Thioredoxins;452
24.3;III. Glutaredoxins;470
24.4;IV. Protein disulfide isomerases;476
24.5;V. Conclusion;479
24.6;Acknowledgments;480
24.7;References;481
25;CHAPTER 12 The Mitochondrial Genome;494
25.1;I. Introduction;495
25.2;II. Characteristics of the mitochondrial genome;496
25.3;III. Mutations affecting the mitochondrial genome;499
25.4;IV. Mitochondrial genome transmission;506
25.5;V. Mitochondrial transformation;509
25.6;Acknowledgments;510
25.7;References;510
26;CHAPTER 13 Oxidative Phosphorylation: Building Blocks and Related Components;518
26.1;I. Introduction;519
26.2;II. Complexes of the mitochondrial respiratory chain;520
26.3;III. Import of nucleus-encoded OXPHOS proteins;536
26.4;IV. Conclusions and perspectives;539
26.5;Acknowledgments;540
26.6;References;540
27;CHAPTER 14 Light-Harvesting Proteins;552
27.1;I. Introduction;553
27.2;II. Structure and composition of the light-harvesting apparatus;554
27.3;III. Light-harvesting proteins;562
27.4;IV. LHC-like proteins;570
27.5;V. Regulation of the light-harvesting complex;574
27.6;Acknowledgments;577
27.7;References;578
28;CHAPTER 15 Photosystem I;590
28.1;I. Introduction;591
28.2;II. Composition of PS I;594
28.3;III. Energy transfer and electron transfer within PS I;597
28.4;IV. Electron transfer to and from PS I;608
28.5;V. Assembly and disassembly of PS I;613
28.6;VI. Frontiers of PS I research using the Chlamydomonas system;614
28.7;Acknowledgments;614
28.8;References;614
29;CHAPTER 16 Photosystem II, a Structural Perspective;622
29.1;I. Introduction;622
29.2;II. Overview of the photosystem II complex;623
29.3;III. Beyond the photosystem II crystal structure;643
29.4;References;643
30;CHAPTER 17 The Cytochrome b[sub(6)]f Complex;652
30.1;I. Introduction;653
30.2;II. Structure of the b[sub(6)]f complex;653
30.3;III. The b[sub(6)]f complex at the crossroads of electron transport and signal transduction;660
30.4;IV. Biogenesis of the b[sub(6)]f complex;668
30.5;V. Conclusion;676
30.6;Acknowledgments;677
30.7;References;677
31;CHAPTER 18 The CF[sub(0)]F[sub(1)] ATP Synthase Complex of Photosynthesis;688
31.1;I. Introduction;689
31.2;II. Composition, structure and specific features of the ATP synthase;689
31.3;III. Mechanistic aspects of the synthesis/hydrolysis of ATP;698
31.4;IV. Concluding remarks;710
31.5;References;711
32;CHAPTER 19 Chaperones and Proteases;720
32.1;I. Introduction;721
32.2;II. Regulation of the heat shock response;722
32.3;III. Small HSPs;723
32.4;IV. HSP33: a redox-regulated chaperone;725
32.5;V. HSP60s;726
32.6;VI. HSP70s;727
32.7;VII. HSP90s;741
32.8;VIII. Elevated levels of sHSPs, HSP60, and HSP70 in Chlamydomonas acidophila;744
32.9;IX. HSP100 proteins function as chaperones and/or components of ATP-dependent proteases;744
32.10;X. FtsH proteases;748
32.11;XI. Lon;749
32.12;XII. DegP and C-terminal processing peptidases;749
32.13;XIII. N-terminal maturation of organelle-encoded proteins;752
32.14;XIV. Peptidases in organellar import and membrane translocation;753
32.15;XV. Intramembrane proteases: Site2 peptidase, PARL/rhomboid, Spp, SppA;755
32.16;XVI. Proteolytic processes in the organelles of Chlamydomonas: whodunnit?;758
32.17;XVII. Conclusion;761
32.18;References;761
33;CHAPTER 20 Biosynthesis of Chlorophylls and Hemes;780
33.1;I. Introduction;781
33.2;II. Outline of tetrapyrrole biosynthesis;782
33.3;III. ALA formation from glutamate;782
33.4;IV. Steps common to the biosynthesis of all tetrapyrroles;791
33.5;V. Steps from uroporphyrinogen III to protoporphyrin IX;794
33.6;VI. Steps specific to chlorophyll formation;797
33.7;VII. Biosynthesis of chlorophyll b;809
33.8;VIII. Minor chlorophyll a derivatives in reaction centers;810
33.9;IX. Chlorophyll degradation and interconversion of chlorophylls a and b;810
33.10;X. The branch from uroporphyrinogen III to siroheme;812
33.11;XI. The branch from protoporphyrin IX to hemes;814
33.12;XII. Heme catabolism;818
33.13;XIII. Regulation;819
33.14;References;824
34;CHAPTER 21 Carotenoids;848
34.1;I. Introduction;848
34.2;II. Occurrence and analysis;849
34.3;III. Biosynthesis;852
34.4;IV. Localization and functional significance;857
34.5;V. Carotenoids as biosynthetic precursors;859
34.6;VI. Outlook;859
34.7;Acknowledgments;860
34.8;References;860
35;CHAPTER 22 State Transitions;868
35.1;I. Introduction;869
35.2;II. What are state transitions?;869
35.3;III. Phosphorylation and mobility of LHCII polypeptides;871
35.4;IV. Regulation of phosphorylation;877
35.5;V. Thylakoid protein kinases;879
35.6;VI. Maintenance of ATP levels through state transitions;885
35.7;VII. Genetic approaches;886
35.8;VIII. Role of state transitions;888
35.9;IX. Conclusions and prospects;888
35.10;Acknowledgments;889
35.11;References;889
36;CHAPTER 23 Photoprotection and High Light Responses;896
36.1;I. Introduction;896
36.2;II. High light-induced damage and repair;898
36.3;III. Regulation of photosynthetic light harvesting by nonphotochemical quenching;902
36.4;IV. Regulation of gene expression and acclimation to high light;905
36.5;Acknowledgments;910
36.6;References;911
37;CHAPTER 24 The Chloroplast Genome;920
37.1;I. Introduction;920
37.2;II. Genome structure and sequence;921
37.3;III. Gene content;927
37.4;IV. DNA replication;929
37.5;V. Genome evolution;931
37.6;VI. Conclusions and perspectives;934
37.7;References;935
38;CHAPTER 25 Chloroplast Transcription;942
38.1;I. Introduction;942
38.2;II. Transcription units: single genes and gene clusters;943
38.3;III. The transcription machinery;944
38.4;IV. Initiation and termination of transcription;951
38.5;V. Regulation of chloroplast transcription;956
38.6;VI. Perspectives;958
38.7;Acknowledgments;958
38.8;References;958
39;CHAPTER 26 Chloroplast RNA Splicing;964
39.1;I. Introduction;964
39.2;II. Group I Introns;965
39.3;III. Group II intron splicing;970
39.4;IV. Are splicing and its regulation essential?;977
39.5;V. Conclusions;978
39.6;Acknowledgments;979
39.7;References;979
40;CHAPTER 27 Chloroplast RNA Processing and Stability;986
40.1;I. Chloroplast RNA processing;987
40.2;II. Chloroplast RNA stability and degradation;998
40.3;III. Conclusions and perspectives;1007
40.4;Acknowledgments;1008
40.5;References;1008
41;CHAPTER 28 Protein Synthesis in the Chloroplast;1016
41.1;I. Introduction;1017
41.2;II. Methodologies used in studies of chloroplast translation;1018
41.3;III. Chloroplast ribosomes;1020
41.4;IV. General chloroplast translation factors;1033
41.5;V. The regulation of translation by light;1037
41.6;VI. Genetic approaches that have identified chloroplast translation factors;1044
41.7;VII. Cis-acting translation elements in chloroplast 5' UTRs;1049
41.8;VIII. mRNA termini may interact during translation;1054
41.9;IX. The localization of protein synthesis;1055
41.10;X. Translation and protein targeting;1057
41.11;XI. Future perspectives;1057
41.12;Acknowledgments;1058
41.13;References;1058
42;CHAPTER 29 The CES Process;1076
42.1;I. Introduction;1077
42.2;II. Assembly of multisubunit photosynthetic protein complexes;1078
42.3;III. CES, a major control step in the biogenesis of photosynthetic proteins;1082
42.4;IV. CES cascades and assembly of multimeric protein complexes;1089
42.5;V. Is CES central to organelle protein expression?;1093
42.6;VI. CES and the nuclear control of chloroplast gene expression;1098
42.7;VII. Conclusion;1102
42.8;Acknowledgments;1102
42.9;References;1102
43;Index;1114
43.1;A;1114
43.2;B;1115
43.3;C;1115
43.4;D;1116
43.5;E;1116
43.6;F;1116
43.7;G;1116
43.8;H;1117
43.9;I;1117
43.10;J;1117
43.11;K;1117
43.12;L;1117
43.13;M;1117
43.14;N;1118
43.15;O;1118
43.16;P;1118
43.17;Q;1119
43.18;R;1119
43.19;S;1119
43.20;T;1120
43.21;U;1120
43.22;V;1120
43.23;W;1120
43.24;X;1120
43.25;Y;1120
43.26;Z;1120