Annual Plant Reviews, Control of Primary Metabolism in Plants (Volume 22)

Control of Primary Metabolism in Plants......Page 1
Contents......Page 7
Contributors......Page 17
Preface......Page 19
1.1 Introduction......Page 23
1.2 Transcript profiling technologies......Page 24
1.3 Transcript profiling workflow......Page 25
1.3.1 Data generation......Page 26
1.3.2 Data management......Page 27
1.3.3.1 Raw data handling......Page 28
1.3.3.2 Normalisation......Page 29
1.3.4.1 Differential expression......Page 31
1.3.4.2 Data mining......Page 32
1.3.4.3 Functional categorisation......Page 34
1.3.5 Data visualisation......Page 35
1.4 What can we learn from transcript profiles performed in a starchless mutant?......Page 37
1.5 Conclusion/perspectives......Page 39
Acknowledgements......Page 40
References......Page 41
2.1 Introduction......Page 46
2.2 Proteomic methodologies......Page 47
2.2.1 Extraction of proteins from plant tissue......Page 48
2.2.2 Separation, display and quantification of proteins......Page 49
2.2.3 Identification of proteins by mass spectrometry......Page 50
2.2.4 Gel-free proteomic approaches......Page 52
2.3.1 Localizing proteins to different tissues......Page 53
2.3.2 Establishing subcellular protein localization: methodologies......Page 55
2.3.3 Mitochondrial and chloroplast proteomes......Page 57
2.3.4 Other subcellular proteomes......Page 61
2.3.5 A stamp of authenticity for the subcellular protein postcode?......Page 62
2.4 Quantitative analyses of the proteome......Page 63
2.4.1 Examples of quantitative proteomics......Page 64
2.4.2 The use of high-throughput measurements of enzyme activity as a proxy for quantitative proteomics......Page 66
2.5 The use of proteomics to investigate post-translational modification of proteins......Page 67
2.5.1 Systematic identification of phosphorylated proteins......Page 68
2.5.2 Systematic identification of protein redox modifications......Page 69
2.6 The use of proteomics to investigate protein–protein interactions......Page 70
2.7 Future perspectives......Page 72
References......Page 74
3.1.1 What is metabolomics?......Page 82
3.1.2 Systemic properties in metabolic networks......Page 83
3.2.1 Historic perspective of plant metabolite analysis......Page 84
3.2.2 Modern instrumentation in metabolite analysis......Page 85
3.2.3 Sample preparation for metabolomics......Page 86
3.2.4.1 The quest for combining sensitivity and selectivity......Page 88
3.2.4.2 Cellular and subcellular metabolomics......Page 90
3.2.4.3 Compound identification......Page 91
3.2.5 Quality control......Page 92
3.3 Metabolomic databases......Page 93
3.4 Pathways, clusters and networks: applications of plant metabolomics......Page 94
3.4.1 Bioengineering of metabolism......Page 95
3.4.2.1 Pathway analysis......Page 96
3.4.2.2 Flux measurements......Page 97
3.4.3 Physiological studies......Page 98
3.4.4 Plant metabolomic methods......Page 99
3.4.5 Food science......Page 100
References......Page 102
4.1 Introduction......Page 107
4.2.2 The plastidic triose-phosphate pool – a metabolic crossway......Page 108
4.2.2.1 Communication between the starch and sucrose biosynthetic pathways via TPT......Page 109
4.3 Nitrogen assimilation......Page 112
4.4 Amino acid and isoprenoid metabolism......Page 115
4.4.2 Shikimic acid pathway and aromatic amino acid biosynthesis......Page 116
4.4.3 Isoprenoid synthesis via the deoxy-xylulose 5-phosphate pathway......Page 118
4.5.1 Mobilization of stored carbon and nitrogen......Page 119
4.5.2 Mechanisms of phloem loading and involvement of transporter proteins......Page 120
4.5.3 Sucrose transporters......Page 121
4.5.5 Genetic modification of phloem loading with assimilates......Page 122
4.6 Phloem unloading in sinks and assimilate transport to developing seeds......Page 123
4.6.2 Uptake of sucrose and amino acids by the developing embryo......Page 124
4.6.4 Sucrose and amino acid import into developing embryos/cotyledons......Page 125
4.7 Assimilate transport and metabolism in sink cells......Page 126
4.7.1 The role of hexose-phosphate import into nongreen plastids......Page 127
4.7.4 Antisense repression and overexpression of NTTs in potato......Page 128
4.7.5 A novel role for Rubisco in developing oilseeds......Page 129
Acknowledgements......Page 130
References......Page 131
5.1 Introduction......Page 143
5.2 Protein kinases......Page 144
5.2.1 Phosphoinositide 3-kinase-like kinases......Page 145
5.3 Protein phosphatases......Page 146
5.3.1 Protein phosphatase 1......Page 147
5.3.2 Protein phosphatase 2A......Page 148
5.3.3 Protein phosphatase 2C......Page 149
5.3.4 Novel protein phosphatases......Page 150
5.3.5.3 Class III cysteine-based protein tyrosine phosphatases......Page 152
5.3.6 RNA polymerase II phosphatases-FCP1 and SCP......Page 153
5.4.1 Phosphospecific binding modules......Page 154
5.4.2 14-3-3 proteins......Page 155
5.4.2.1 14-3-3 structures and function......Page 156
5.4.2.2 14-3-3 roles and control......Page 158
5.5.1 Nutrient sensing and signalling through conserved protein kinases......Page 159
5.5.2 Nitrate reductase......Page 161
5.5.4 Sucrose phosphate synthase and trehalose phosphate synthase......Page 162
5.5.6 Starch synthase and starch branching enzyme......Page 163
5.5.8 Nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase......Page 164
Acknowledgements......Page 165
References......Page 166
6.1 Introduction......Page 172
6.2 The reactivity of the sulfhydryl group......Page 173
6.4 Thioredoxins......Page 177
6.4.1 Thioredoxin isoforms......Page 178
6.4.2 Reductants of thioredoxins (sources of reducing power)......Page 180
6.4.3 Targets of thioredoxins (oxidants of thioredoxin)......Page 183
6.4.4 Control of chloroplast enzymes by thioredoxin......Page 184
6.4.5 Translation of chloroplast mRNA......Page 187
6.4.7 Control of mitochondrial proteins......Page 188
6.4.8 Removal of reactive oxygen species......Page 189
6.4.9 Seed germination......Page 191
6.5 Glutaredoxins......Page 192
6.6 Protein-disulfide isomerases......Page 195
References......Page 197
7.1 Introduction......Page 209
7.2 Ribulose-1,5-bisphosphate carboxylase-oxygenase......Page 212
7.3 Glyceraldehyde-3-phosphate dehydrogenase......Page 216
7.4 Fructose-1,6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase......Page 219
7.5 Phosphoribulokinase......Page 221
7.6.1 Transketolase......Page 223
7.6.2. Aldolase......Page 224
7.7 Supramolecular complexes of the Calvin cycle......Page 225
7.8 Conclusions......Page 228
References......Page 229
8.1 Introduction......Page 241
8.2 PPCK genes and their roles......Page 242
8.3 Signalling pathways that control PPCK expression in CAM and C4 plants......Page 246
8.4 The ‘bacterial-type’ PEPC......Page 250
8.5 Conclusions......Page 251
References......Page 252
9.2 Pathways of sucrose biosynthesis in leaves......Page 256
9.2.1 Sucrose synthesis in leaves during the day......Page 258
9.2.2 Sucrose synthesis in leaves at night......Page 259
9.3.1 The conversion of triose-phosphate to hexose-phosphate......Page 260
9.3.2 The hexose-phosphate pool and UDP-glucose pyrophosphorylase......Page 262
9.4.1 Sucrose-phosphate synthase......Page 263
9.4.2 Sucrose-phosphatase......Page 267
9.4.3 Evidence for a metabolon in sucrose biosynthesis......Page 268
9.5 Integrated pathway control......Page 269
9.6 Future perspectives......Page 270
References......Page 272
10.1 Introduction......Page 280
10.2 Synthesis of bacterial glycogen......Page 281
10.3.1 Substrate supply and activation......Page 282
10.3.2 Amylose synthesis......Page 285
10.3.3 Amylopectin synthesis......Page 286
10.4.1 Isoamylases are directly involved in the synthesis of amylopectin but also during starch mobilization......Page 288
10.4.2 Glucan phosphorylation is the key signal of starch degradation in both leaves and tubers......Page 289
10.4.4 Starch metabolism is tightly controlled by several levels of regulation......Page 290
10.5 Control of starch biosynthesis in monocotyledonous species......Page 291
10.5.1 Genes in the rice genome......Page 293
10.6.2 The Chlamydomonas single cell can account for both transitory or storage starch synthesis......Page 294
10.6.3 What have we learned from Chlamydomonas?......Page 295
10.6.4 Similarity and differences between starch metabolism in plants and algae......Page 296
10.6.5 The future of starch research in green algae......Page 297
10.7.1 Bacterial cells may have a primitive starch synthesizing machinery......Page 298
10.7.2 UDPglucose-based systems that produce starch......Page 299
10.8 Control of starch biosynthesis......Page 300
10.9 Opportunities for the manipulation of starch synthesis and structure......Page 302
References......Page 303
11.2.1 Tricarboxylic acid cycle and associated enzymes......Page 312
11.2.2 Electron transport chain complexes I–V......Page 316
11.2.3 Additional electron transport chain and associated components......Page 317
11.3.1 Phosphorylation – dephosphorylation......Page 321
11.3.2 Dithiol-disulfide interconversion......Page 322
11.3.3 Other oxidative modifications......Page 323
11.3.4 Supramolecular complexes......Page 324
11.4 Integration of mitochondrial metabolism with other metabolic pathways......Page 325
11.4.1 Mitochondrial metabolism during photosynthesis......Page 326
11.4.3 Mitochondrial fatty acid synthesis......Page 327
11.4.4 The glyoxylate cycle and lipid respiration......Page 328
11.5.2 Mechanisms to scavenge mitochondrial ROS......Page 329
11.5.3 Mechanisms to avoid mitochondrial ROS generation......Page 331
11.6.1 GABA shunt......Page 333
11.6.3 Formate dehydrogenase......Page 334
11.6.4 Mitochondrial aldehyde dehydrogenases......Page 335
11.6.6 Nucleoside diphosphate kinase......Page 336
11.7 Concluding remarks......Page 337
References......Page 338
12.1 Introduction......Page 347
12.2 Integration of C and N metabolism in leaves......Page 348
12.3 Control of nitrate assimilation rates and the C/N interaction......Page 351
12.4 Pathway coordination and the C/N signal transduction network......Page 353
12.5 Modelling the C/N interaction......Page 355
12.5.1 Construction of a tentative model to explore the sensitivities in the GS and GOGAT reactions......Page 357
References......Page 364
13.1 Introduction......Page 370
13.2 Sulfate uptake and distribution......Page 373
13.2.1 Transcriptional regulation of transport......Page 374
13.2.2 Post-translation controls......Page 375
13.3.2.1 Sulfate activation by ATP sulfurylase......Page 376
13.3.2.2 Sulfate reduction by APS reductase......Page 377
13.3.3. Transcriptional regulation and coordination with C and N pathways......Page 378
13.4 Control of flux through the assimilatory pathway – cysteine synthesis......Page 379
13.4.2 Metabolic control of the ‘cysteine synthase’ complex......Page 380
13.4.4 The role of O-acetylserine as an ‘inducer’ of gene expression......Page 381
13.4.5 A model for control of cysteine synthesis......Page 383
13.5 Control of flux to the various sinks after cysteine biosynthesis......Page 384
13.6 Summary......Page 386
References......Page 387
Index......Page 395