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The Handbook of Plant Metabolomics. Molecular Plant Biology - Product Image

The Handbook of Plant Metabolomics. Molecular Plant Biology

  • ID: 2329950
  • April 2013
  • 448 Pages
  • John Wiley and Sons Ltd

Metabolomics is the analysis of all metabolites such as metabolic intermediates, hormones and so on, in a given system such as a cell, an organ or a whole organism. It is complementary to the genomics and proteomic analysis of a system and an essential building block towards the understanding of a whole biological system. Being a relatively new approach, a number of techniques have been recently developed in order to experimentally analyse metabolites and many researchers are expanding into this field. Knowledge about the metabolic status of a system is critical for its comprehensive understanding and metobolomics is an important tool for systems biologists.

This is the newest title in the successful Molecular Plant Biology Handbook Series. Just like the other titles in the series, The Handbook of Plant Metabolomics presents an excellent overview of different approaches and techniques in the subject. Contributors are either from ivy-league research institutions or from companies developing new technologies in this dynamic and fast-growing field. With its approach to introduce current techniques in plant metabolomics to a wider audience and with many labs and companies considering to introduce metabolomics for their research, this book is intended for molecular biologists, geneticists, biotechnologists, plant physiologists, gene technologists, protein chemists, biotechnological industry personel and the pharmaceutical industry.

With uniform chapter design with summaries and comprehensive glossary, the Kahl books are in addition a trusted brand for the plant science community.

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Preface XVII

List of Contributors XIX

Part I Central Metabolism 1

1 Metabolic Profiling of Plants by GC–MS 3
Camilla B. Hill and Ute Roessner

1.1 Introduction 3

1.2 Methods and Protocols 7

1.2.1 Sample Preparation 7

1.2.2 Chemical Derivatization: Methoxymation and Silylation 9

1.2.3 GC–MS Analysis 10

1.2.3.1 Procedure to Acquire GC–MS Data 11

1.2.4 Data Preprocessing and Export 12

1.3 Applications of the Technology 15

1.4 Perspectives 17

References 18

2 Isotopologue Profiling – Toward a Better Understanding of Metabolic Pathways 25
Wolfgang Eisenreich, Claudia Huber, Erika Kutzner, Nihat Knispel, and Nicholas Schramek

2.1 Introduction 25

2.2 Methods and Protocols to Determine Isotopologues 31

2.2.1 Mass Spectrometry 31

2.2.2 Protocols for Isotopologue Profiling by GC–MS 36

2.2.3 NMR Spectroscopy 38

2.2.4 Protocols for Isotopologue Profiling by NMR 41

2.2.5 Deconvolution of Isotopologue Data 43

2.2.6 Expanding the Metabolic Space by Retrobiosynthetic Analysis 45

2.3 Applications 46

2.3.1 Experiments Using ½U-13C6_Glucose 46

2.3.2 Experiments Using 13CO2 47

2.4 Perspectives 53

References 54

3 Nuclear Magnetic Resonance Spectroscopy for Plant Metabolite Profiling 57
Sonia van der Sar, Hye Kyong Kim, Axel Meissner, Robert Verpoorte, and Young Hae Choi

3.1 Introduction 57

3.2 Methods and Protocols 59

3.2.1 Sample Preparation 59

3.2.2 Data Acquisition 60

3.2.3 Standard 1H-NMR Spectroscopy 61

3.2.4 J-Resolved Spectroscopy 61

3.2.5 Data Analysis 61

3.3 Applications 62

3.3.1 1D 1H-NMR Spectroscopy 62

3.3.2 2D NMR Spectroscopy 63

3.3.3 Magic Angle Spinning 70

3.4 Perspectives 71

References 72

4 Comprehensive Two-Dimensional Gas Chromatography for Metabolomics 77
Katja Dettmer, Martin F. Almstetter, Christian J. Wachsmuth, and Peter J. Oefner

4.1 Introduction 77

4.2 Methods and Protocols 81

4.2.1 Instrumentation 81

4.2.2 Sample Preparation and Analysis 82

4.2.3 Data Processing 83

4.2.4 Metabolic Fingerprinting 83

4.2.5 Quantitative Analysis of Selected Metabolites 84

4.3 Applications of the Technology 85

4.3.1 Data Analysis 85

4.3.2 Literature 88

4.4 Perspectives 89

References 90

5 MALDI Mass Spectrometric Imaging of Plants 93
Ale9s Svato9s and Hans-Peter Mock

5.1 Introduction 93

5.1.1 Sample Preparation 96

5.1.2 Data Acquisition 98

5.1.3 Data Processing 98

5.2 Methods and Protocols 99

5.2.1 Sample Preparation and Handling 99

5.2.2 Matrix Deposition 100

5.2.3 MALDI-MS Imaging Measurement 103

5.3 Imaging Intact Tissues and Objects 105

5.4 Future Perspectives 109

References 109

6 Medicago truncatula Root and Shoot Metabolomics: Protocol for the Investigation of the Primary Carbon and Nitrogen Metabolism Based on GC–MS 111
Vlora Mehmeti, Lena Fragner, and Stefanie Wienkoop

6.1 Introduction 111

6.2 Methods and Protocols 112

6.2.1 Equipment and Software 112

6.2.2 Buffers and Chemicals 112

6.2.3 Plant Material and Harvest 113

6.2.4 Extraction 114

6.2.5 Derivatization 115

6.2.6 GC–MS Setup for the Analysis 115

6.2.7 Metabolite Identification and Quantification: Data Matrix Processing 116

6.2.8 Data Mining 119

6.3 Applications of the Technology 119

6.4 Perspectives 121

References 123

Part II Secondary and Lipid Metabolism 125

7 Study of the Volatile Metabolome in Plant–Insect Interactions 127
Georg J.F. Weingart, Nora C. Lawo, Astrid Forneck, Rudolf Krska, and Rainer Schuhmacher

7.1 Introduction 127

7.1.1 Plant–Insect Interactions 127

7.1.2 Significance of Volatile Plant Metabolites 128

7.1.3 Study of the Plant Volatile Metabolome in Plant–Insect Interactions 128

7.2 Methods and Protocols 135

7.2.1 Permanent Breed of Insects 135

7.2.2 Cultivation of Grapevine Plants and Inoculation with Phylloxera 136

7.2.3 Sampling and Quenching of Plant Tissue (Roots and Leaves) 138

7.2.4 Milling and Weighing of Plant Tissue (Roots and Leaves) 140

7.2.5 Measurement – Automated HS-SPME Extraction and GC–MS Analysis 143

7.2.6 Data Processing with AMDIS 145

7.2.7 Statistics/Chemometrics 147

7.3 Applications of the Technology 148

7.4 Perspectives 149

References 150

8 Metabolomics in Herbal Medicine Research 155
Lie-Fen Shyur, Chiu-Ping Liu, and Shih-Chang Chien

8.1 Introduction 155

8.2 Methods and Protocols 158

8.2.1 Materials 158

8.2.2 Procedures 160

8.3 Applications 168

8.4 Perspectives 169

References 170

9 Integrative Analysis of Secondary Metabolism and Transcript Regulation in Arabidopsis thaliana 175
Fumio Matsuda and Kazuki Saito

9.1 Introduction 175

9.2 Methods and Protocols 177

9.2.1 Metabolome Analysis of Plant Secondary Metabolites 177

9.2.2 Preparation of Combined Data Matrix 180

9.2.3 Data Mining 180

9.3 Applications of the Technology 183

9.4 Perspectives 187

References 190

10 Liquid Chromatographic–Mass Spectrometric Analysis of Flavonoids 197
Maciej Stobiecki and Piotr Kachlicki

10.1 Introduction 197

10.1.1 Role of Flavonoids and Their Derivatives in Biological Systems 197

10.1.2 Preparation of Biological Material for Metabolomic Analysis and/or Metabolite Profiling 199

10.1.3 Instrumental Considerations 201

10.2 Methods and Protocols: Liquid Chromatography–Mass Spectrometry of Flavonoids 206

10.2.1 General Remarks 206

10.2.2 Plant Cultivation Conditions 208

10.2.3 Preparation of Biological Material with Biotechnological Methods (Callus, Cell, or Hairy Root Cultures) 208

10.2.4 Extraction of Plant Tissue or Biotechnologically Prepared Material 208

10.2.5 Solid-Phase Extraction of Culture Medium or Apoplastic Fluids 209

10.2.6 Preparation of Samples for LC–MS Analyses 210

10.2.7 Chromatographic Protocols for Separation of Flavonoid Glyconjugates 210

10.2.8 Control of Ionization Parameters During Mass Spectrometric Analysis and Identification of Compounds During LC–MS Metabolite Profiling 211

10.3 Applications of the Technology 211

10.4 Perspectives 211

References 212

11 Introduction to Lipid (FAME) Analysis in Algae Using Gas Chromatography–Mass Spectrometry 215
Takeshi Furuhashi and Wolfram Weckwerth

11.1 Introduction 215

11.2 Methods and Experimental Protocol 216

11.2.1 Extraction 216

11.2.2 Bound and Free Fatty Acids 217

11.2.3 Pigments 217

11.2.4 Contaminants 219

11.2.5 Derivatization 219

11.2.6 GC–MS System 220

11.2.7 Identification 220

11.2.8 Protocols 221

11.2.9 GC–MS Instrument and Conditions 223

11.3 Application and Perspective 223

References 224

12 Multi-Gene Transformation for Pathway Engineering of Secondary Metabolites 227
Hideyuki Suzuki, Eiji Takita, Kiyoshi Ohyama, Satoru Sawai, Hikaru Seki, Nozomu Sakurai, Toshiya Muranaka, Masao Ishimoto, Hiroshi Sudo, Kazuki Saito, and Daisuke Shibata

12.1 Introduction 227

12.2 Methods and Protocols 233

12.2.1 Chemicals 233

12.2.2 Plasmid Construction of Multi-Gene Transformation 233

12.2.3 Preparation of Dual Terminator (DT) Fragment by PCR-Based Overlap Extension Method 233

12.2.4 Plasmid Construction of pUHR KS CSPS Thsp 236

12.2.5 Construction of pHSG299 CSPS 35S-CYP88-DT (Figure 12.2a) 236

12.2.6 Construction of pHSG299 CSPS 35S-CYP72-DT2 (Figure 12.2a) 237

12.2.7 Construction of pHSG299-CYP93(RNAi)-DT (Figure 12.2a) 238

12.2.8 Construction of pUHR KS CSPS Thsp-CYP88-CYP72-CYP93 (RNAi) 239

12.2.9 Transformation of Soybean by Particle Bombardment 239

12.2.10 GC-MS Analysis for Triterpene Glycone 241

12.2.11 GC-MS Conditions 242

12.3 Application of Technology 242

12.4 Perspectives 243

References 243

Part III Metabolomics and Genomics 245

13 Metabolomics-Assisted Plant Breeding 247
Alexander Herrmann and Nicolas Schauer

13.1 Introduction 247

13.2 Method 249

13.3 Applications of the Technology 251

13.4 Perspective 253

References 254

14 Conducting Genome-Wide Association Mapping of Metabolites 255
Susanna Atwell and Daniel J. Kliebenstein

14.1 Introduction 255

14.2 Methods and Protocols 256

14.2.1 Biological Question to Be Addressed 256

14.2.2 Chemistry to Study 256

14.2.3 Species Choice 258

14.2.4 Should I Utilize an Additional Perturbation? 260

14.2.5 Conducting the Phenotype Measurements 261

14.2.6 Computational Platform to Use for Analysis 261

14.2.7 Candidate Gene Selection 265

14.2.8 Candidate Gene Validation 266

14.3 Applications 267

14.4 Perspectives 268

References 268

Part IV Metabolomics and Bioinformatics 273

15 Metabolite Clustering and Visualization of Mass Spectrometry Data Using One-Dimensional Self-Organizing Maps 275
Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Ivo Feussner, and Peter Meinicke

15.1 Introduction 275

15.2 Methods and Protocols 276

15.2.1 Data Import 277

15.2.2 Clustering 277

15.2.3 Cluster Analysis 280

15.3 Applications of the Technology 281

15.4 Perspectives 286

References 286

16 Metabolite Identification and Computational Mass Spectrometry 289
Steffen Neumann, Florian Rasche, Sebastian Wolf, and Sebastian B€ocker

16.1 Introduction 289

16.2 Annotation and Identification of Metabolites 290

16.2.1 Exact Mass Search in Compound Libraries 291

16.2.2 Deriving the Elemental Composition from MS1 292

16.2.3 Elemental Composition from MS2 and MSn 293

16.2.4 In Silico Library Search with MetFrag 294

16.2.5 Reference Spectral Library Lookup 299

16.3 Perspectives 302

References 303

17 Using COVAIN to Analyze Metabolomics Data 305
Xiaoliang Sun and Wolfram Weckwerth

17.1 Introduction 305

17.2 Methods 308

17.2.1 Data Preprocessing 308

17.2.2 Uni- and Bivariate Statistical Methods for Individual Metabolite-Level Analysis 311

17.2.3 Multivariate Statistical Methods for Group-Level Analysis 312

17.2.4 Network-Level Analysis 313

17.2.5 Influences of Data Preprocessing on Statistical Analysis Results 313

17.3 Application 314

17.4 Perspective 320

References 320

18 Mass Spectral Search and Analysis Using the Golm Metabolome Database 321
Jan Hummel, Nadine Strehmel, Christian B€olling, Stefanie Schmidt, Dirk Walther, and Joachim Kopka

18.1 Introduction 321

18.2 Methods and Protocols: the GMD and Supported Data Analysis Workflows 322

18.2.1 The GMD Data Entities 322

18.2.2 The Text Search Queries 325

18.2.3 The Mass Spectrum Query Submission and Analysis Options 325

18.2.4 Interpreting the Mass Spectral Analysis Results 329

18.2.5 The Web Services at GMD 336

18.2.6 The GMD Download Options 338

18.3 Applications and Perspectives 341

References 342

Glossary 345

Index 415

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Günter Kahl is Professor for Plant Molecular Biology at the Biocenter of Johann Wolfgang Goethe-University of Frankfurt/Main, Germany. After gaining his PhD in plant biochemistry, he spent two postdoctoral years at Michigan State University, East Lansing, USA, joining Professor Joe Varner, and at the California Institute of Technology, Pasadena, California, with Professor James Bonner. His main research interests are:. - Sequencing and analysis of fungal, plant and animal genomes. - Transcriptome analysis in pro- and eukaryotic organisms. - Technology development. Günter Kahl is the author of more than 250 scientific journal publications and several book publications including all titles of the successful Molecular Plant Biology Handbook series, and currently holds the CSO position at GenXPro GmbH, a company specializing in novel technologies in genomics and transcriptomics, located at the Frankfurt Innovation Centre for Biotechnology (FIZ), Frankfurt/Main, Germany.. . Wolfram Weckwerth is Professor and founding chair of the Department of Molecular Systems Biology (MOSYS) at the University of Vienna, Austria. He holds a diploma in chemistry and a PhD in biochemistry, both from the Technical University Berlin, Germany. His main research interests are:. - The development of genome-wide metabolomics and proteomics/phosphoproteomics technologies as elementary systems biology techniques, high throughput profiling (HTP) in systems biology, data integration; combining experimental approaches with multivariate statistics, pattern recognition, modeling of metabolism, and functional genome interpretation: synergetics. - The genotype-environment-phenotype-equation: plant ecology and phenotypic plasticity including stress, growth, developmental and nutritional physiology. - Plant-microbe-interaction and medicinal plants. - Green Systems Biology: application of systems biology approaches in ecology, evolution and biotechnology

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