Plant Metabolomics

Section I Analytical Technology I.1 Gas Chromatography Mass Spectrometry 3(18) J. KOPKA 1 Introduction 3(2) 2 GC-MS Profiling Technology in a Nutshell 5(5) 3 Short Excursion into Nomenclature and Definitions 10(3) 4 Present Challenges of GC-MS Profiling 13(4) References 17(4) I.2 Current Status and Forward Looking Thoughts on LC/MS Metabolomics 21(12) L.W. SUMNER 1 Introduction 21(3) 2 Chromatography Theory 24(1) 3 Limitations of Current Metabolic Profiling Approaches and Proposed Solutions to Advance Metabolomics 25(3) 4 Future Directions and Forward-Looking Thoughts 28(2) References 30(3) I.3 Plant Metabolomics Strategies Based upon Quadrupole Time of Flight Mass Spectrometry (QTOF-MS) 33(16) H.A. VERHOEVEN, C.H. RIC DE VOS, R.J. BIND, and R.D. HALL 1 Introduction 33(1) 2 The Technology 34(3) 3 Data Analysis 37(1) 4 Application of QTOF MS-based Plant Metabolomics Analyses 38(8) 5 Conclusions and Future Prospects 46(1) References 46(3) I.4 Capillary HPLC 49(16) T. IKEGAMI, E. FUKUSAKI, and N. TANAKA 1 Introduction 49(1) 2 Monolithic Silica Columns for Micro HPLC 49(5) 3 Applications of Monolithic Silica Columns to Metabolomics 54(1) 4 Two-Dimensional HPLC 55(4) 5 Combination of Reversed-Phase HPLC and Other Separation Modes 59(2) 6 Outlook 61(1) References 61(4) I.5 Capillary HPLC Coupled to Electrospray Ionization Quadrupole Time-of-flight Mass Spectrometry 65(16) S. CLEMENS, C. BÖTTCHER, M. FRANZ, E. WILLSCHER, E.V. ROEPENACK-LAHAYE, and D. SCHEEL 1 Introduction 65(2) 2 Extraction, Chromatography and Mass Spectrometry 67(5) 3 Potential and Limitations 72(5) 4 Conclusions and Outlook 77(1) References 78(3) I.6 NMR Spectroscopy in Plant Metabolomics 81(12) J.L. WARD and M.H. BEALE 1 Introduction 81(1) 2 High-throughput Screening by ID 1H-NMR 82(2) 3 Data Analysis 84(1) 4 Two-dimensional NMR 85(1) 5 Stable Isotope Labelling 86(1) 6 Hyphenated NMR 87(1) 7 Discussion: Applying NMR to Plant Metabolomics 88(1) References 89(4) I.7 Hetero-nuclear NMR-based Metabolomics 93(12) J. KIKUCHI and T. HIRAYAMA 1 Introduction 93(1) 2 Historical Aspects of NMR Studies of Plant Metabolism 93(1) 3 1H-NMR-based Metabolomics 94(1) 4 Use of Stable Isotope Labeling Technique to Enable Monitoring of the Dynamic Movement of Metabolites 94(1) 5 Approach for Hetero-nuclear NMR-based Metabolomics 95(3) 6 Prospects for the Future 98(1) References 99(6) Section II Bioinformatics II.1 Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data 105(12) B. MEHROTRA and P. MENDES 1 Introduction 105(2) 2 Databases 107(3) 3 Data Visualization 110(1) 4 Data Analysis 111(1) 5 Conclusion 112(1) References 113(4) II.2 Chemometrics in Metabolomics - An Introduction 117(12) J. TRYGG, J. GULLBERG, JOHANSSON, P. JONSSON, and T. MORITZ 1 Introduction 117(1) 2 Theory and Methods 118(7) 3 Example: Metabolomics Study on Arabidopsis Mutants 125(1) 4 Summary and Future Prospectives 126(1) References 127(2) II.3 Map Editor for the Atomic Reconstruction of Metabolism (ARM) 129(12) M. ARITA, Y. FUJIWARA, and Y. NAKANISHI 1 Introduction 129(2) 2 Definition of Metabolic Information 131(2) 3 Metabolic Map Editor 133(4) 4 Applications 137(2) 5 Conclusions 139(1) References 139(2) II.4 AraCyc: Overview of an Arabidopsis Metabolism Database and its Applications for Plant Research 141(14) S.Y. RHEE, P. ZHANG, H. FOERSTER, and C. TISSIER 1 Introduction 141(1) 2 Database Content 142(3) 3 Search, Browse, and Analyze Functionalities 145(4) 4 Applications of AraCyc 149(3) 5 Current Issues and Future Directions 152(1) 6 Conclusions 152(1) References 153(2) II.5 KaPPA-View: A Tool for Integrating Transcriptomic and Metabolomic Data on Plant Metabolic Pathway Maps 155(10) T. TOKIMATSU, N. SAKURAI, H. SUZUKI, and D. SHIBATA 1 Introduction 155(1) 2 General Features of the KaPPA-View Tool 155(3) 3 Plant Metabolic Pathway Maps 158(1) 4 Integration of Transcriptomic and Metabolomic Data on Pathway Maps 159(1) 5 Comparison with Other Databases and Tools 159(1) 6 Limitations and Future Improvements 160(2) 7 Conclusions 162(1) References 163(2) II.6 KNApSAcK: A Comprehensive Species-Metabolite Relationship Database 165(20) Y. SHINBO, Y. NAKAMURA, M. ALTAF-UL-AMIN, H. ASAHI, K. KUROKAWA, M. ARITA, K. SAITO, D. OHTA, D. SHIBATA, and S. KANAYA 1 Introduction 165(1) 2 Search Options of the KNApSAcK Database 166(6) 3 Statistics of the Database 172(5) 4 Classification Based on Common Metabolites 177(2) 5 Conclusion and Remarks 179(1) 6 Access to KNApSAcK 179(1) References 180(5) Section III Applications III.1 Systems Biology: A Renaissance of the Top-down Approach for Plant Analysis 185(14) F. CARRARI, N. SCHAUER, L. WILLMITZER, and A.R. FERNIE 1 Introduction 185(1) 2 Re-emergence of Top-down Thinking 186(1) 3 Systems Biology in Non-plant Systems 186(2) 4 Systems Biology in Plant Systems 188(4) 5 Dynamic Profiling in Plant Cells 192(3) 6 Conclusions and Future Perspectives 195(1) References 195(4) III.2 Systems-based Analysis of Plant Metabolism by Integration of Metabolomics with Transcriptomics 199(12) M.Y. HIRAI, T. TOHGE, and K. SAITO 1 Introduction 199(1) 2 Understanding Whole Plant Metabolism - Our Aims and Strategy 199(1) 3 Metabolome and Transcriptome Analyses 200(1) 4 Studies on Sulfur Metabolism 201(5) 5 Studies on Anthocyanin Metabolism 206(2) 6 Conclusions 208(1) References 209(2) III.3 Targeted Profiling of Fatty Acids and Related Metabolites 211(18) T.R. LARSON and I.A. GRAHAM 1 Introduction 211(2) 2 Metabolite Profiling Techniques Used to Study Plant Lipid Metabolism 213(10) 3 Future Developments 223(1) References 224(5) III.4 Metabolic Profiling and Quantification of Carotenoids and Related Isoprenoids in Crop Plants 229(14) P.D. FRASER and P.M. BRAMLEY 1 Introduction 229(4) 2 Analytical Methodologies Employed in the Analysis of Carotenoids 233(4) 3 Examples of Carotenoid/isoprenoid Profiling 237(3) 4 Conclusions 240(1) References 240(3) III.5 Metabolomics and Gene Identification in Plant Natural Product Pathways 243(18) R.A. DIXON, L. ACHNINE, B.E. DEAVOURS, and M. NAOUMKINA 1 Introduction 243(1) 2 Gene Discovery - Past and Present Strategies 243(3) 3 Enzyme Promiscuity in Natural Product Pathways 246(1) 4 Examples of the Use of Metabolomics in the Elucidation of Gene Function 247(6) 5 Single Cell or Isolated Tissue Metabolomics 253(3) 6 Concluding Remarks 256(1) References 256(5) III.6 Metabolomic Analysis of Catharanthus roseus Using NMR and Principal Component Analysis 261(16) H.K. KIM, Y.H. CHOI, and R. VERPOORTE 1 Introduction 261(1) 2 Experimental Consideration for Metabolomics Using NMR 262(4) 3 Application of NMR for Plant Metabolome 266(7) 4 Principal Component Analysis 273(2) 5 Concluding Remarks 275(1) References 275(2) III.7 Metabolomics of Plant Secondary Compounds: Profiling of Catharanthus Cell Cultures 277(14) M. ORESIC, H. RISCHER, and K.-M. OKSMAN-CALDENTEY 1 Introduction 277(1) 2 Metabolomics as a Platform to Study Plant Secondary Metabolites 278(2) 3 Case Study: Metabolic Profiling of Catharanthus roseus Cells 280(5) 4 Protocol 285(1) 5 Perspectives 286(1) References 287(4) III.8 The Taxus Metabolome and the Elucidation of the Taxol® Biosynthetic Pathway in Cell Suspension Cultures 291(20) R.E.B. KETCHUM and R.B. CROTEAU 1 Introduction 291(3) 2 Results and Discussion 294(12) 3 Protocol 306(1) 4 Conclusion 307(1) References 308(3) III.9 The Use of Non-targeted Metabolomics in Plant Science 311(16) T. DASKALCHUK, P. AHIAHONU, D. HEATH, and Y. YAMAZAKI 1 Introduction 311(2) 2 Fundamental Investigations into Plant Metabolomics 313(11) 3 Conclusion 324(1) References 324(3) III.10 Plant Metabolite Profiling for Industrial Applications 327(14) R.N. TRETHEWEY 1 Introduction 327(1) 2 The Metabolome 327(1) 3 Profiling Technologies 328(4) 4 High Throughput Metabolite Profiling 332(3) 5 Industrial Applications 335(3) 6 Outlook 338(1) References 338(3) Subject Index 341