Plant Metabolomics Book

Section I Analytical Technology

I.1 Gas Chromatography Mass Spectrometry

J. Kopka

1 Introduction

2 GC-MS Profiling Technology in a Nutshell

3 Short Excursion into Nomenclature and Definitions

4 Present Challenges of GC-MS Profiling

References

I.2 Current Status and Forward Looking Thoughts on LC/MS Metabolomics

L.W. Sumner

1 Introduction

2 Chromatography Theory

3 Limitations of Current Metabolic Profiling Approaches and Proposed Solutions to Advance Metabolomics

4 Future Directions and Forward-Looking Thoughts

References

I.3 Plant Metabolomics Strategies Based upon Quadrupole Time of Flight Mass Spectrometry(QTOF-MS)

H.A. Verhoeven, C.H. Ric de Vos, R.J. Bino, and R.D. Hall

1 Introduction

2 The Technology

3 Data Analysis

4 Application of QTOF MS-based Plant Metabolomics Analyses

5 Conclusions and Future Prospects

References

I.4 Capillary HPLC

T. Ikegami, E. Fukusaki, and N. Tanaka

1 Introduction

2 Monolithic Silica Columns for Micro HPLC

3 Applications of Monolithic Silica Columns to Metabolomics

4 Two-Dimensional HPLC

5 Combination of Reversed Phase HPLC and Other Separation Modes

6 Outlook

References

I.5 Capillary HPLC Coupled to Electrospray Ionization Quadrupole Time-of-flight Mass Spectrometry

S. Clemens, C. Boettcher, M. Franz, E. Willscher, E. v. Roepenack-Lahaye, and D. Scheel

1 Introduction

2 Extraction, Chromatography and Mass Spectrometry

3 Potential and Limitations

4 Conclusions and Outlook

References

I.6 NMR Spectroscopy in Plant Metabolomics

J.L. Ward and M.H. Beale

1 Introduction

2 High-throughput Screening by 1D 1H-NMR

3 Data Analysis

4 Two-dimensional NMR

5 Stable Isotope Labelling

6 Hyphenated NMR

7 Discussion: Applying NMR to Plant Metabolomics

References

I.7 Hetero-nuclear NMR-based Metabolomics

J. Kikuchi and T. Hirayama

1 Introduction

2 Historical Aspects of NMR Studies of Plant Metabolism

3 1H-NMR-based Metabolomics

4 Use of Stable Isotope Labeling Technique to Enable Monitoring of the Dynamic Movement of Metabolites

5 Approach for Hetero-nuclear NMR-based Metabolomics

6 Prospects for the Future

References

Section II Bioinformatics

II.1 Bioinformatics Approaches to Integrate Metabolomics and Other Systems Biology Data.

B. Mehrotra and P. Mendes

1 Introduction

2 Databases

3 Data Visualization

4 Data Analysis

5 Conclusion

References

II.2 Chemometrics in Metabolomics—An Introduction

J. Trygg, J. Gullberg, A.I. Johansson, P. Jonsson, and T. Moritz

1 Introduction

2 Theory and Methods

3 Example: Metabolomics Study on Arabidopsis Mutants

4 Summary and Future Prospectives

References

II.3 Map Editor for the Atomic Reconstruction of Metabolism (ARM)

M. Arita, Y. Fujiwara, and Y. Nakanishi

1 Introduction

2 Definition of Metabolic Information

3 Metabolic Map Editor

4 Applications

5 Conclusions

References

II.4 AraCyc: Overview of an Arabidopsis Metabolism Database and its Applications for Plant Research

S.Y. Rhee, P. Zhang, and H. Foerster

1 Introduction

2 Database Content

3 Search, Browse, and Analyze Functionalities

4 Applications of AraCyc

5 Current Issues and Future Directions

6 Conclusions

References

II.5 Kappa-View: A Tool for Integrating Transcriptomic and Metabolomic Data on Plant Metabolic Pathway Maps

T. Tokimatsu, N. Sakurai, H. Suzuki, and D. Shibata

1 Introduction

2 General Features of the KaPPA-View Tool

3 Plant Metabolic Pathway Maps

4 Integration of Transcriptomic and Metabolomic Data on Pathway Maps

5 Comparison with Other Databases and Tools

6 Limitations and Future Improvements

7 Conclusions

References

II.6 KNApSAcK: A Comprehensive Species-Metabolite Relationship Database

Y. Shinbo, Y. Nakamura, M. Altaf-Ul-Amin, H. Asahi, K. Kurokawa, H. Suzuki, N. Sakurai, A. Oikawa, M. Kitayama, M. Yano, M.Y. Hirai, T. Tokimatsu, M. Arita, K. Saito, D. Ohta, D. Shibata, and S. Kanaya

1 Introduction

2 Search Options of the KNApSAcK Database

3 Statistics of the Database

4 Classification Based on Common Metabolites

5 Conclusion and Remarks

6 Access to KNApSAcK

References

Section III Applications

III.1 Systems Biology: A Renaissance of the Top-down Approach for Plant Analysis

F. Carrari, N. Schauer, L. Willmitzer, and A.R Fernie

1 Introduction

2 Re-emergence of Top-down Thinking

3 Systems Biology in Non-plant Systems

4 Systems Biology in Plant Systems

5 Dynamic Profiling in Plant Cells

6 Conclusions and Future Perspectives

References

III.2 Systems-based Analysis of Plant Metabolism by Integration of Metabolomics with Transcriptomics

M.Y. Hirai, T. Tohge, and K. Saito

1 Introduction

2 Understanding Whole Plant Metabolism—Our Aims and Strategy

3 Metabolome and Transcriptome Analyses

4 Studies on Sulfur Metabolism

5 Studies on Anthocyanin Metabolism

6 Conclusions

References

III.3Targeted Profiling of Fatty Acids and Related Metabolites

T.R. Larson and I.A. Graham

1 Introduction

2 Metabolite Profiling Techniques Used to Study Plant Lipid Metabolism

3 Future Developments

References

III.4 Metabolic Profiling and Quantification of Carotenoids and Related Isoprenoids in Crop Plants

P.D. Fraser and P.M. Bramley

1 Introduction

2 Analytical Methodologies Employed in the Analysis of Carotenoids

3 Examples of Carotenoid/isoprenoid Profiling

4 Conclusions

References

III.5 Metabolomics and Gene Identification in Plant Natural Product Pathways

R.A. Dixon, L. Achnine, B.E. Deavours, and M. Naoumkina

1 Introduction

2 Gene Discovery—Past and Present Strategies

3 Enzyme Promiscuity in Natural Product Pathways

4 Examples of the Use of Metabolomics in the Elucidation of Gene Function

5 Single Cell or Isolated Tissue Metabolomics

6 Concluding Remarks

References

III.6 Metabolomic Analysis of Catharanthus roseus Using NMR and Principal Component Analysis

H.K. Kim, Y.H. Choi, and R. Verpoorte

1 Introduction

2 Experimental Consideration for Metabolomics Using NMR

3 Application of NMR for Plant Metabolome

4 Principal Component Analysis

5 Concluding Remarks

References

III.7 Metabolomics of Plant Secondary Compounds: Profiling of Catharanthus Cell Cultures

M. Orešic, H, Rischer, and K.-M. Oksman-Caldentey

1 Introduction

2 Metabolomics as a Platform to Study Plant Secondary Metabolites

3 Case Study: Metabolic Profiling of Catharanthus roseus Cells

4 Prool

5 Perspectives

References

III.8 The Taxus Metabolome and the Elucidation of Taxol® Biosynthetic Pathway in Cell Suspension Cultures

R.E.B. Ketchum and R.B. Croteau

1 Introduction

2 Results and Discussion

3 Prool

4 Conclusion

References

III.9 The Use of Non-targeted Metabolomics in Plant Science

T. Daskalchuk, P. Ahiahonu, D. Heath, and Y. Yamazaki

1 Introduction

2 Fundamental Investigations into Plant Metabolomics

3 Conclusion

References

III.10 Plant Metabolite Profiling for Industrial Applications

R.N. Trethewey

1 Introduction

2 The Metabolome

3 Profiling Technologies

4 High Throughput Metabolite Profiling

5 Industrial Applications

6 Outlook

References

Subject Index