The Handbook of Plant Metabolomics

433 Pages·2013·14.974 MB·English

by  Wolfram Weckwerth, Guenter Kahl

Editedby
WolframWeckwerth
andGünterKahl
TheHandbookofPlant
Metabolomics
TitlesoftheSeries“MolecularPlantBiologyHandbookSeries”
Kahl,G.,Meksem,K.(eds.)
TheHandbookofPlantFunctionalGenomics
ConceptsandProtocols
2008
ISBN:978-3-527-31885-8
Meksem,K.,Kahl,G.(eds.)
TheHandbookofPlantMutationScreening
MiningofNaturalandInducedAlleles
2010
ISBN:978-3-527-32604-4
Meksem,K.,Kahl,G.(eds.)
TheHandbookofPlantGenomeMapping
GeneticandPhysicalMapping
2005
ISBN:978-3-527-31116-3
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Edited by Wolfram Weckwerth and Günter Kahl
The Handbook of Plant Metabolomics
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j
VII
Contents
Preface XVII
ListofContributors XIX
PartI CentralMetabolism 1
1 MetabolicProfilingofPlantsbyGC–MS 3
CamillaB.HillandUteRoessner
1.1 Introduction 3
1.2 MethodsandProtocols 7
1.2.1 SamplePreparation 7
1.2.1.1 Sampling 7
1.2.1.2 HomogenizationandExtraction 7
1.2.1.3 ProcedureforPolarExtractionofMetabolites 8
1.2.2 ChemicalDerivatization:MethoxymationandSilylation 9
1.2.2.1 ProcedurefortheChemicalDerivatizationofPlantExtracts 9
1.2.3 GC–MSAnalysis 10
1.2.3.1 ProceduretoAcquireGC–MSData 11
1.2.4 DataPreprocessingandExport 12
1.2.4.1 ProcedureforPostacquisitionDataPreprocessing 12
1.2.4.2 DataAnalysisandStatistics 14
1.2.4.3 ProcedureforPostacquisitionDataAnalysis 15
1.3 ApplicationsoftheTechnology 15
1.4 Perspectives 17
References 18
2 IsotopologueProfiling–TowardaBetterUnderstanding
ofMetabolicPathways 25
WolfgangEisenreich,ClaudiaHuber,ErikaKutzner,NihatKnispel,
andNicholasSchramek
2.1 Introduction 25
2.2 MethodsandProtocolstoDetermineIsotopologues 31
2.2.1 MassSpectrometry 31
2.2.2 ProtocolsforIsotopologueProfilingbyGC–MS 36
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VIII Contents
2.2.2.1 Protein-BoundAminoAcids 36
2.2.2.2 MetabolicIntermediatesandPolarProducts 37
2.2.2.3 Carbohydrates 37
2.2.3 NMRSpectroscopy 38
2.2.4 ProtocolsforIsotopologueProfilingbyNMR 41
2.2.5 DeconvolutionofIsotopologueData 43
2.2.6 ExpandingtheMetabolicSpacebyRetrobiosyntheticAnalysis 45
2.3 Applications 46
2.3.1 ExperimentsUsing½U-13C (cid:2)Glucose 46
6
2.3.2 ExperimentsUsing13CO 47
2
2.4 Perspectives 53
References 54
3 NuclearMagneticResonanceSpectroscopyforPlant
MetaboliteProfiling 57
SoniavanderSar,HyeKyongKim,AxelMeissner,RobertVerpoorte,
andYoungHaeChoi
3.1 Introduction 57
3.2 MethodsandProtocols 59
3.2.1 SamplePreparation 59
3.2.1.1 HarvestingPlantMaterial 60
3.2.1.2 Drying 60
3.2.1.3 Extraction 60
3.2.2 DataAcquisition 60
3.2.3 Standard1H-NMRSpectroscopy 61
3.2.4 J-ResolvedSpectroscopy 61
3.2.5 DataAnalysis 61
3.3 Applications 62
3.3.1 1D1H-NMRSpectroscopy 62
3.3.2 2DNMRSpectroscopy 63
3.3.2.1 J-ResolvedSpectroscopy 65
3.3.2.2 COSYandTOCSY 67
3.3.2.3 HMBCandHMQC/HSQC 68
3.3.2.4 NOESYorROESY(CAMELSPIN) 69
3.3.2.5 DOSY 69
3.3.3 MagicAngleSpinning 70
3.4 Perspectives 71
References 72
4 ComprehensiveTwo-DimensionalGasChromatography
forMetabolomics 77
KatjaDettmer,MartinF.Almstetter,ChristianJ.Wachsmuth,
andPeterJ.Oefner
4.1 Introduction 77
4.2 MethodsandProtocols 81
j
Contents IX
4.2.1 Instrumentation 81
4.2.2 SamplePreparationandAnalysis 82
4.2.3 DataProcessing 83
4.2.4 MetabolicFingerprinting 83
4.2.5 QuantitativeAnalysisofSelectedMetabolites 84
4.3 ApplicationsoftheTechnology 85
4.3.1 DataAnalysis 85
4.3.2 Literature 88
4.4 Perspectives 89
References 90
5 MALDIMassSpectrometricImagingofPlants 93
Ale9sSvato9sandHans-PeterMock
5.1 Introduction 93
5.1.1 SamplePreparation 96
5.1.2 DataAcquisition 98
5.1.3 DataProcessing 98
5.2 MethodsandProtocols 99
5.2.1 SamplePreparationandHandling 99
5.2.1.1 IntactTissues 99
5.2.1.2 Cryosectioning 99
5.2.2 MatrixDeposition 100
5.2.2.1 Paintbrush(Figure5.2) 100
5.2.2.2 Sublimation(Figure5.3) 102
5.2.3 MALDI-MSImagingMeasurement 103
5.2.3.1 BrukerUltraflexInstruments 103
5.2.3.2 WatersMALDIMicroMX 104
5.3 ImagingIntactTissuesandObjects 105
5.4 FuturePerspectives 109
References 109
6 MedicagotruncatulaRootandShootMetabolomics:Protocol
fortheInvestigationofthePrimaryCarbonandNitrogenMetabolism
BasedonGC–MS 111
VloraMehmeti,LenaFragner,andStefanieWienkoop
6.1 Introduction 111
6.2 MethodsandProtocols 112
6.2.1 EquipmentandSoftware 112
6.2.2 BuffersandChemicals 112
6.2.3 PlantMaterialandHarvest 113
6.2.4 Extraction 114
6.2.5 Derivatization 115
6.2.6 GC–MSSetupfortheAnalysis 115
6.2.7 MetaboliteIdentificationandQuantification:DataMatrix
Processing 116
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X Contents
6.2.8 DataMining 119
6.3 ApplicationsoftheTechnology 119
6.4 Perspectives 121
References 123
PartII SecondaryandLipidMetabolism 125
7 StudyoftheVolatileMetabolomeinPlant–InsectInteractions 127
Georg J.F.Weingart,NoraC.Lawo,AstridForneck,Rudolf Krska,
andRainerSchuhmacher
7.1 Introduction 127
7.1.1 Plant–InsectInteractions 127
7.1.2 SignificanceofVolatilePlantMetabolites 128
7.1.3 StudyofthePlantVolatileMetabolomeinPlant–InsectInteractions 128
7.1.3.1 SettingUpofBiologicalExperiments 129
7.1.3.2 Sampling,Quenching,andSamplePreparation 130
7.1.3.3 HeadspaceExtractionandMeasurementbyGC–MS 131
7.1.3.4 DataHandling 134
7.1.3.5 BiologicalInterpretation 135
7.2 MethodsandProtocols 135
7.2.1 PermanentBreedofInsects 135
7.2.2 CultivationofGrapevinePlantsandInoculationwithPhylloxera 136
7.2.2.1 Materials 136
7.2.2.2 Procedures 136
7.2.3 SamplingandQuenchingofPlantTissue(RootsandLeaves) 138
7.2.3.1 SamplingandQuenchingofRootTips 138
7.2.3.2 SamplingandQuenchingofGrapevineLeaves 139
7.2.4 MillingandWeighingofPlantTissue(RootsandLeaves) 140
7.2.4.1 MillingandWeighingofRootSamples 140
7.2.4.2 MillingandWeighingofLeafSamples 141
7.2.5 Measurement–AutomatedHS-SPMEExtraction
andGC–MSAnalysis 143
7.2.5.1 Materials 143
7.2.5.2 SPMEMethod 143
7.2.5.3 GCMethod 144
7.2.5.4 MSSettings 144
7.2.6 DataProcessingwithAMDIS 145
7.2.6.1 AnIn-HouseReferenceLibraryHastobeEstablishedinAdvance 145
7.2.6.2 GenerationofRICalibrationFile 146
7.2.6.3 BatchJobAnalysisfortheSimultaneousProcessingofMultiple
SampleChromatograms 146
7.2.7 Statistics/Chemometrics 147
7.2.7.1 UnivariateStatistics 147
7.2.7.2 MultivariateStatistics 148
j
Contents XI
7.3 ApplicationsoftheTechnology 148
7.4 Perspectives 149
References 150
8 MetabolomicsinHerbalMedicineResearch 155
Lie-FenShyur,Chiu-PingLiu,andShih-ChangChien
8.1 Introduction 155
8.2 MethodsandProtocols 158
8.2.1 Materials 158
8.2.1.1 Reagents 158
8.2.1.2 Equipment 159
8.2.2 Procedures 160
8.2.2.1 SampleHandlingforMedicinalPlants 160
8.2.2.2 SamplePreparationforLC–MSAnalysis 160
8.2.2.3 LC–MSAnalysis 161
8.2.2.4 HPLC–PhotodiodeArray(PDA)MSSetupandAnalysis 161
8.2.2.5 GC–MSAnalysis 162
8.2.2.6 PlantExtractPreparationforGC–MSAnalysis 163
8.2.2.7 GC–MSParametersandAnalysis 164
8.2.2.8 LC–MSandGC–MSDataAnalysis 165
8.2.2.9 LC–SPE–NMRAnalysis 166
8.2.2.10 SamplePreparationandLC–SPE–NMRAnalysis 167
8.2.2.11 HPLC–SPE–NMRDataAnalysis 168
8.3 Applications 168
8.4 Perspectives 169
References 170
9 IntegrativeAnalysisofSecondaryMetabolismandTranscript
RegulationinArabidopsisthaliana 175
FumioMatsudaandKazukiSaito
9.1 Introduction 175
9.2 MethodsandProtocols 177
9.2.1 MetabolomeAnalysisofPlantSecondaryMetabolites 177
9.2.1.1 SamplePreparation 177
9.2.1.2 DataAcquisition 178
9.2.1.3 PreparationofMetaboliteAccumulationDatafromtheRaw
ChromatogramData 179
9.2.2 PreparationofCombinedDataMatrix 180
9.2.2.1 PreparationofGeneExpressionData 180
9.2.2.2 CombinationofDataMatrices 180
9.2.3 DataMining 180
9.2.3.1 BL-SOMAnalysis 180
9.2.3.2 CorrelationAnalysis 181
9.2.3.3 PrincipalComponentAnalysisandApplicationofOther
DataMiningTechniques 183