Series Editor: Stefan Hohmann - Springer978-3-540-74719-2/1.pdf · BioCentrum-DTU Technical University of Denmark Søltofts Plads DK-2800 Kgs. Lyngby Denmark e-mail: [email protected]

Topics in Current Genetics

Series Editor: Stefan Hohmann

Jens Nielsen · Michael C. Jewett (Eds.)

MetabolomicsA Powerful Tool in Systems Biology

With 53 Figures, 13 in Color; and 14 Tables

123

Professor Dr. Jens Nielsen

Dr. Michael C. Jewett

Center for Microbial BiotechnologyBioCentrum-DTUTechnical University of DenmarkSøltofts PladsDK-2800 Kgs. LyngbyDenmarke-mail: [email protected]

[email protected]

The cover illustration depicts pseudohyphal filaments of the ascomycete Saccharomyces cerevisiae thatenable this organism to forage for nutrients. Pseudohyphal filaments were induced here in a wild-type haploid MATa Σ1278b strain by an unknown readily diffusible factor provided by growth inconfrontation with an isogenic petite yeast strain in a sealed petri dish for two weeks and photographedat 100X magnification (provided by Xuewen Pan and Joseph Heitman).

ISBN 978-3-540-74718-5

DOI 10.1007/978-3-540-74719-2

e-ISBN 978-3-540-74719-2

Topics in Current Genetics ISSN 1610-2096

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Table of contents

The role of metabolomics in systems biology ......................................................1 Jens Nielsen and Michael C. Jewett...................................................................1

Abstract .........................................................................................................1 1 Metabolomics .............................................................................................1 2 Applications of metabolomics....................................................................3 3 The role of metabolomics in systems biology ............................................4 4 Outline of this book....................................................................................6 References .....................................................................................................8

Analytical methods from the perspective of method standardization ............11 Silas G. Villas-Bôas, Albert Koulman, and Geoffrey A. Lane ........................11

Abstract .......................................................................................................11 1 Introduction ..............................................................................................11 2 Pre-analytical variability ..........................................................................13

2.1 Biological variability ........................................................................13 2.2 Variability introduced during sampling ............................................14 2.3 Variability introduced during sample processing .............................19

3 Intra-analytical variability ........................................................................28 3.1 GC-MS..............................................................................................29 3.2 ESI-MS .............................................................................................37 3.3 Conclusions.......................................................................................43

4 Post-analytical issues................................................................................43 5 Final remarks............................................................................................44 Acknowledgments.......................................................................................45 References ...................................................................................................45 Abbreviations ..............................................................................................51

Reporting standards............................................................................................53 Nigel Hardy and Helen Jenkins .......................................................................53

Abstract .......................................................................................................53 1 Introduction ..............................................................................................53

1.1 Data handling in metabolomics ........................................................54 2 Standards, models, and formats................................................................56 3 Initiatives in metabolomics data standards...............................................60

3.1 MIAMET ..........................................................................................60 3.2 ArMet................................................................................................61 3.3 SMRS................................................................................................61 3.4 MSI ...................................................................................................62

4 Reporting standards in other fields...........................................................62 4.1 Transcriptomics ................................................................................62 4.2 Proteomics ........................................................................................64

VIII Table of contents

5 Cross-domain standards ........................................................................... 64 6 Issues in metabolomics standards............................................................. 66

6.1 The detailed nature of standards ....................................................... 66 6.2 Controlled vocabularies and ontologies............................................ 68 6.3 Chemical identity.............................................................................. 69

7 Conclusions.............................................................................................. 70 References................................................................................................... 70

The Golm Metabolome Database: a database for GC-MS based metabolite profiling ............................................................................................. 75

Jan Hummel, Joachim Selbig, Dirk Walther, and Joachim Kopka.................. 75 Abstract ....................................................................................................... 75 1 Introduction.............................................................................................. 75

1.1 Pathway databases ............................................................................ 77 1.2 Cheminformatics databases .............................................................. 78 1.3 Databases dedicated to metabolite profiling ..................................... 79 1.4 The Golm Metabolome Database (GMD) ........................................ 80

2 Database objects....................................................................................... 80 3 Information exchange between databases ................................................ 81 4 The main work flows of metabolite profiling........................................... 82

4.1 The metabolite profiling work flow: from sample to metabolite fingerprint and profile............................................................................. 83 4.2 The metabolite mapping work flow: from metabolite to specific and selective GC-MS mass fragment...................................................... 85

5 The main database objects........................................................................ 87 5.1 Modelling the “MST” database object.............................................. 87 5.2 Modelling the “chemical substance” database object ....................... 88

6 Outlook..................................................................................................... 90 References................................................................................................... 91 List of abbreviations.................................................................................... 95

Reconstruction of dynamic network models from metabolite measurements ...................................................................................................... 97

Matthias Reuss, Luciano Aguilera-Vázquez, Klaus Mauch ............................ 97 Abstract ....................................................................................................... 97 1 Introduction.............................................................................................. 97 2 Quantitative measurements of intracellular metabolites .......................... 99 3 Use of metabolite measurements for identification of dynamic models ....................................................................................................... 103

3.1 Modular decomposition of the network.......................................... 103 3.2 In silico identification of whole cell metabolite dynamics through evolutionary algorithms and parallel computing ..................... 118 3.3 Identification of kinetic rate expression from series of steady state observations.................................................................................. 122

4. Summary and outlook ........................................................................... 123 References................................................................................................. 124

Table of contents IX

Toward metabolome-based 13C flux analysis: a universal tool for measuring in vivo metabolic activity ................................................................129

Nicola Zamboni .............................................................................................129 Abstract .....................................................................................................129 1 Introduction ............................................................................................129 2 Fundamentals of metabolic flux analysis ...............................................132 3 Principles of labeling experiments .........................................................133 4 Current practice of stationary 13C flux analysis......................................135

4.1 Experimental design .......................................................................135 4.2 From analytes to 13C labeling patterns ............................................136 4.3 From 13C labeling patterns to fluxes ...............................................138

5 Toward metabolome-based 13C flux analysis .........................................144 5.1 Experimental proof-of-concept .......................................................144 5.2 Analytics: lessons from metabolomics ...........................................145 5.3 Current developments .....................................................................147

6 Conclusions ............................................................................................151 Acknowledgements ...................................................................................151 References .................................................................................................151 List of abbreviations..................................................................................157

Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae .............................................159

Michael C. Jewett, Michael A.E. Hansen, and Jens Nielsen..........................159 Abstract .....................................................................................................159 1 Yeast as a model system for metabolomics............................................159 2 Metabolite analysis workflow ................................................................161 3 Chemical analysis...................................................................................162

3.1 Quenching.......................................................................................162 3.2 Extraction........................................................................................162 3.3 Analytical methods .........................................................................163 3.4 Standardization ...............................................................................165

4 Data analysis ..........................................................................................165 4.1 Pre-processing.................................................................................166 4.2 Statistical analysis...........................................................................169 4.3 Classification ..................................................................................175 4.4 Genetic programming .....................................................................175 4.5 SpectConnect ..................................................................................176

5 Data integration ......................................................................................177 6 Future outlook ........................................................................................180 Acknowledgements ...................................................................................180 References .................................................................................................180

X Table of contents

E. coli metabolomics: capturing the complexity of a “simple” model .......... 189 Martin Robert, Tomoyoshi Soga and Masaru Tomita ................................... 189

Abstract ..................................................................................................... 189 1 Introduction............................................................................................ 189 2 Experimental methods............................................................................ 190

2.1 Quenching of metabolism and metabolite extraction...................... 191 2.2 Main analytical methods tested with E. coli ................................... 193 3.1 Groundwork.................................................................................... 198 3.2 Combining concentration data with enzyme activity and flux measurements ....................................................................................... 201 3.3 Emerging metabolomic studies in E. coli ....................................... 202

4 Evaluating the size of the E. coli metabolome ....................................... 203 4.1 Hints from genome-based models .................................................. 203 4.2 Experimental clues.......................................................................... 203 4.3 Improving metabolite identification ............................................... 204

5 Architecture/anatomy of the E. coli metabolome................................... 206 5.1 Metabolite architecture ................................................................... 206 5.2 Pathway architecture....................................................................... 206

6 E. coli metabolomics as a powerful tool for functional genomics ......... 207 6.1 Metabolic footprinting .................................................................... 208 6.2 Enzyme discovery using non-targeted metabolomics..................... 208 6.3 Deorphanizing enzymatic activities and filling-in metabolic pathway holes ....................................................................................... 212 6.4 Phenotype microarrays as reporters of metabolic phenotype.......... 212

7 Metabolomics to facilitate metabolic engineering of E. coli .................. 213 8 Metabolomics in flux analysis................................................................ 215 9 Adaptive evolution in E. coli, metabolomics, and metabolic phenotype .................................................................................................. 215 10 Metabolic models of E. coli: the role of metabolomics........................ 216 11 Databases and resources....................................................................... 218 12 Data integration and visualization........................................................ 221 13 Future prospects and developments ..................................................... 222 14 Concluding remarks ............................................................................. 223 Acknowledgement..................................................................................... 223 References................................................................................................. 224 Abbreviations ............................................................................................ 234

The exo-metabolome in filamentous fungi ...................................................... 235 Ulf Thrane, Birgitte Andersen, Jens C. Frisvad, Jørn Smedsgaard................ 235

Abstract ..................................................................................................... 235 1 Introduction............................................................................................ 235 2 Exo-metabolome and taxonomy............................................................. 236 3 Exo-metabolome and fungal growth ...................................................... 237 4 Visualisation of the exo-metabolome..................................................... 239 5 Extraction of the exo-metabolome ......................................................... 240

Table of contents XI

6 Analysis of the exo-metabolome by high performance liquid chromatography.........................................................................................242 7 Direct infusion electrospray mass spectrometry for profiling ................247 8 Outlook – a polyphasic approach ...........................................................248 Acknowledgements ...................................................................................249 References .................................................................................................249

The importance of anatomy and physiology in plant metabolomics.............253 Ute Roessner and Filomena Pettolino............................................................253

Abstract .....................................................................................................253 1 Introduction ............................................................................................253

1.1 Importance of plants .......................................................................253 1.2 Plant metabolomics.........................................................................254

2 Plant anatomy.........................................................................................255 2.1 Whole plant anatomy ......................................................................255 2.2 Cell anatomy...................................................................................256

3 Plant physiology – Challenges for plant metabolomics..........................260 3.1 Photosynthesis ................................................................................260 3.2 Photorespiration ..............................................................................260 3.3 Transpiration...................................................................................262 3.4 Starch and other storage products ...................................................262 3.5 Cell wall synthesis ..........................................................................263 3.6 Secondary metabolites ....................................................................266

4 Unique aspects of plant research ............................................................267 4.1 Functional genomics .......................................................................267 4.2 Breeding and QTL analysis ............................................................268 4.3 Genetic engineering ........................................................................270

5 Recent, current and future of plant metabolomics..................................272 5.1 Successful applications ...................................................................272

6 Future .....................................................................................................274 References .................................................................................................274

Index ...................................................................................................................279

List of contributors

Aguilera-Vázquez, Luciano Depto.de Biotecnología, Universidad Politécnica de Pachuca, Ex-Hacienda de Sta. Barbara, CP 43830, Municipio de Zenpoala, Hgo, Mexico

Andersen, Birgitte

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark

Frisvad, Jens C.

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark

Hansen, Michael A. E.

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark

Hardy, Nigel

Department of Computer Science, University of Wales, Aberystwyth, Peng-lais, Aberystwyth SY23 3DB, United Kingdom [email protected]

Hummel, Jan

Max Planck Institute of Molecular Plant Physiology (MPI-MP), Am Muehlen-berg 1, 14476 Potsdam-Golm, Germany

Jenkins, Helen

Department of Computer Science, University of Wales, Aberystwyth, Peng-lais, Aberystwyth SY23 3DB, United Kingdom

Jewett, Michael C.

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark

Kopka, Joachim

Max Planck Institute of Molecular Plant Physiology (MPI-MP), Am Muehlen-berg 1, 14476 Potsdam-Golm, Germany [email protected]

Koulman, Albert

AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palm-erston North 4442, New Zealand.

XIV

Lane, Geoffrey A. AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palm-erston North 4442, New Zealand.

Mauch, Klaus

Insilico Biotechnology AG, Nobelstrasse. 15, D-70569 Stuttgart Nielsen, Jens

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark [email protected]

Pettolino, Filomena

School of Botany, The University of Melbourne, 3010 Victoria, Australia Reuss, Matthias

Institute of Biochemical Engineering and Centre of Systems Biology, Univer-sity Stuttgart, Allmandring 31, D-70569 Stuttgart [email protected]

Robert, Martin

Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata, 997-0017 Japan [email protected]

Roessner, Ute

Australian Centre for Plant Functional Genomics, School of Botany, The Uni-versity of Melbourne, 3010 Victoria, Australia [email protected]

Selbig, Joachim

University of Potsdam, Institute of Biochemistry and Biology, c/o MPI-MP, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany

Smedsgaard, Jørn

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark

Soga, Tomoyoshi

Institute for Advanced Biosciences, Keio University, 403-1 Daihoji, Tsuruoka, Yamagata, 997-0017 Japan

Thrane, Ulf

Center for Microbial Biotechnology, BioCentrum-DTU, Technical University of Denmark, Søltofts Plads 221, DK-2800 Kgs. Lyngby, Denmark [email protected]

List of contributors XV

Villas-Bôas, Silas G.

AgResearch Limited, Grasslands Research Centre, Private Bag 11008, Palm-erston North 4442, New Zealand. [email protected]

Walther, Dirk

Max Planck Institute of Molecular Plant Physiology (MPI-MP), Am Muehlen-berg 1, 14476 Potsdam-Golm, Germany

Zamboni, Nicola

Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland [email protected]