Plant Metabolomics (eBook)

Preface 6
Contents 7
List of Contributors 13
Section I Analytical Technology 20
I.1 Gas ChromatographyMass Spectrometry 21
1 Introduction 21
2 GC-MS Pro.ling Technology in a Nutshell 23
3 Short Excursion into Nomenclature and De.nitions 28
4 Present Challenges of GC-MS Pro.ling 31
References 35
I.2 Current Status and Forward Looking Thoughts on LC/ MSMetabolomics 39
1 Introduction 39
2 Chromatography Theory 42
3 Limitations of CurrentMetabolic Pro.ling Approaches and Proposed Solutions to AdvanceMetabolomics 43
4 Future Directions and Forward-Looking Thoughts 46
References 48
I.3 PlantMetabolomics Strategies Based upon Quadrupole Time of FlightMass Spectrometry ( QTOF- MS) 51
1 Introduction 51
2 TheTechnology 52
3 Data Analysis 55
4 Application of QTOF MS-based PlantMetabolomics Analyses 56
5 Conclusions and Future Prospects 64
References 64
I.4 Capillary HPLC 67
1 Introduction 67
2 Monolithic Silica Columns for Micro HPLC 67
3 Applications ofMonolithic Silica Columns toMetabolomics 72
4 Two-Dimensional HPLC 73
5 Combination of Reversed-Phase HPLC and Other SeparationModes 77
6 Outlook 79
References 79
I.5 Capillary HPLC Coupled to Electrospray Ionization Quadrupole Time- of- . ightMass Spectrometry 82
1 Introduction 82
2 Extraction, Chromatography andMass Spectrometry 84
3 Potential and Limitations 89
4 Conclusions and Outlook 94
References 95
I.6 NMR Spectroscopy in PlantMetabolomics 97
1 Introduction 97
2 High-throughput Screening by 1D H-NMR 98
3 Data Analysis 100
4 Two-dimensional NMR 101
5 Stable Isotope Labelling 102
6 HyphenatedNMR 103
7 Discussion: Applying NMR to PlantMetabolomics 104
References 105
I.7 Hetero-nuclear NMR-basedMetabolomics 108
1 Introduction 108
2 Historical Aspects of NMR Studies of PlantMetabolism 108
3 H-NMR-basedMetabolomics 109
4 Use of Stable Isotope Labeling Technique to Enable Monitoring of the DynamicMovement ofMetabolites 109
5 Approach for Hetero-nuclear NMR-basedMetabolomics 110
6 Prospects for the Future 113
References 114
Section II Bioinformatics 117
II.1 Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data 118
1 Introduction 118
2 Databases 120
3 Data Visualization 123
4 Data Analysis 124
5 Conclusion 125
References 126
II.2 Chemometrics inMetabolomics – An Introduction 129
1 Introduction 129
2 Theory andMethods 130
3 Example: Metabolomics Study on ArabidopsisMutants 137
4 Summary and Future Prospectives 138
References 139
II.3 Map Editor for the Atomic Reconstruction ofMetabolism ( ARM) 141
1 Introduction 141
2 Definition ofMetabolic Information 143
3 MetabolicMap Editor 145
4 Applications 149
5 Conclusions 151
References 151
II.4 AraCyc: Overview of an ArabidopsisMetabolism Database and its Applications for Plant Research 152
1 Introduction 152
2 DatabaseContent 153
3 Search, Browse, and Analyze Functionalities 156
4 Applications of AraCyc 160
5 Current Issues and Future Directions 163
6 Conclusions 163
References 164
II.5 KaPPA-View: A Tool for Integrating Transcriptomic andMetabolomic Data on PlantMetabolic PathwayMaps 166
1 Introduction 166
2 General Features of the KaPPA-View Tool 166
3 PlantMetabolic PathwayMaps 169
4 Integration of Transcriptomic andMetabolomic Data on PathwayMaps 170
5 Comparison with Other Databases and Tools 170
6 Limitations and Future Improvements 171
7 Conclusions 173
References 174
II.6 KNApSAcK: A Comprehensive Species-Metabolite Relationship Database 175
1 Introduction 175
2 Search Options of the KNApSAcK Database 176
3 Statistics of the Database 182
4 Classi.cation Based on CommonMetabolites 187
5 Conclusion and Remarks 189
6 Access to KNApSAcK 189
References 190
Section III Applications 192
III.1 Systems Biology: A Renaissance of the Top-down Approach for Plant Analysis 193
1 Introduction 193
2 Re-emergence of Top-down Thinking 194
3 Systems Biology in Non-plant Systems 194
4 Systems Biology in Plant Systems 196
5 Dynamic Pro.ling in Plant Cells 200
6 Conclusions and Future Perspectives 203
References 203
III.2 Systems-based Analysis of PlantMetabolism by Integration ofMetabolomics with Transcriptomics 207
1 Introduction 207
2 UnderstandingWhole PlantMetabolism – Our Aims and Strategy 207
3 Metabolome and Transcriptome Analyses 208
4 Studies on SulfurMetabolism 209
5 Studies on AnthocyaninMetabolism 214
6 Conclusions 216
References 217
III.3 Targeted Pro.ling of Fatty Acids and RelatedMetabolites 218
1 Introduction 218
2 Metabolite Pro.ling Techniques Used to Study Plant LipidMetabolism 220
3 Future Developments 230
References 231
III.4 Metabolic Pro.ling and Quanti.cation of Carotenoids and Related Isoprenoids in Crop Plants 236
1 Introduction 236
2 AnalyticalMethodologies Employed in the Analysis of Carotenoids 240
3 Examples of Carotenoid/isoprenoid Pro.ling 244
4 Conclusions 247
References 247
III.5 Metabolomics and Gene Identi.cation in Plant Natural Product Pathways 250
1 Introduction 250
2 Gene Discovery – Past and Present Strategies 250
3 Enzyme Promiscuity in Natural Product Pathways 253
4 Examples of the Use ofMetabolomics in the Elucidation of Gene Function 254
5 Single Cell or Isolated TissueMetabolomics 260
6 Concluding Remarks 263
References 263
III.6 Metabolomic Analysis of Using NMR and Principal Component Analysis 267
1 Introduction 267
2 Experimental Consideration forMetabolomics Using NMR 268
3 Application of NMR for PlantMetabolome 272
4 Principal Component Analysis 279
5 Concluding Remarks 281
References 281
III.7 Metabolomics of Plant Secondary Compounds: Pro.ling of Catharanthus Cell Cultures 283
1 Introduction 283
2 Metabolomics as a Platform to Study Plant SecondaryMetabolites 284
3 Case Study:Metabolic Profiling of Catharanthus roseus Cells 286
4 Protocol 291
5 Perspectives 292
References 293
III.8 The TaxusMetabolome and the Elucidation of the Taxol®* Biosynthetic Pathway in Cell Suspension Cultures 296
1 Introduction 296
2 Results and Discussion 299
3 Protocol 311
4 Conclusion 312
References 313
III.9 The Use of Non-targetedMetabolomics in Plant Science 315
1 Introduction 315
2 Fundamental Investigations into PlantMetabolomics 317
3 Conclusion 328
References 328
III.10 PlantMetabolite Pro.ling for Industrial Applications 330
1 Introduction 330
2 TheMetabolome 330
3 Pro.ling Technologies 331
4 High ThroughputMetabolite Pro.ling 335
5 Industrial Applications 338
6 Outlook 341
References 341
Subject Index 343