Annual Plant Reviews Volume 43: Biology of Plant Metabolomics

450 Pages·2011·13.33 MB·English

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ANNUAL PLANT REVIEWS
VOLUME 43
i
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DEDICATION
I would like to dedicate this book to the memory of my mother, Sally Hall,
whoasaprimaryschoolteacherandanavidloverofnatureinstilledinme,
at a very early age, her particular interest in wild and garden plants. One
of my earliest memories as a child was when we were once walking in the
woodsonourfarmandshegavemeawoodsorrelleaf(Oxalisacetosella)to
eat. I marvelled at the pleasant acidity. But she then also gave me a clover
leaf(Trifoliumpretense)toeat,bothtoemphasizehowthingsthatlooksimilar
can actually be inherently (and unpleasantly) very different and also as a
warningthatIshouldnoteatanythingIwasnottotallysureof.Thiswasmy
first sensory metabolomics experiment, at the age of 3, and my fascination
forplantshasneverebbedsince.
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ANNUAL PLANT REVIEWS
VOLUME 43
Biology of Plant Metabolomics
Edited by
Robert D. Hall
PlantResearchInternational,WageningenUniversityandResearch
Centre(Wageningen-UR),POBox16,6700AAWageningen,
TheNetherlands;
CentreforBioSystemsGenomics,POBox98,Wageningen,
TheNetherlands;
NetherlandsMetabolomicsCentre,Einsteinweg55,2333CCLeiden,
TheNetherlands.
A John Wiley & Sons, Ltd., Publication
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Thiseditionfirstpublished2011(cid:1)C 2011byBlackwellPublishingLtd.
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LibraryofCongressCataloging-in-PublicationData
Biologyofplantmetabolomics/editedbyRobertHall.
p.cm.–(Annualplantreviews;v.43)
Includesbibliographicalreferencesandindex.
ISBN978-1-4051-9954-4(hardcover:alk.paper) 1.Plants–Metabolism. I.Hall,
RobertD.(RobertDavid),1958– II.Series:Annualplantreviews;v.43.
QK881.B5452011
572(cid:2).42–dc22
2010040815
AcataloguerecordforthisbookisavailablefromtheBritishLibrary.
Thisbookispublishedinthefollowingelectronicformats:ePDF(9781444339932);
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(cid:1)
Setin10/12ptPalatinobyAptaraR Inc.,NewDelhi,India
1 2011
Coverillustration:ThetropicalfruitRambutan(Nepheliumlappaceum)iswellknowforis
succulenceandexquisitetaste.However,aswithmanyplants,aswellasprovidingus
withfood,variouspartsoftheplantsuchastheseedsandbarkalsoprovideuswithdyes,
soapsandmedicinals,thusillustratingthehugebiochemicaldiversitythatnatureoffers
us.Photo:RobertD.Hall,dailymarketLuangPrabang,PRLao.
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AnnualPlantReviews
Aseriesforresearchersandpostgraduatesintheplantsciences.Eachvolume
inthisseriesfocusesonathemeoftopicalimportanceandemphasisisplaced
onrapidpublication.
EditorialBoard:
Prof.JeremyA.Roberts(Editor-in-Chief),PlantScienceDivision,Schoolof
Biosciences,UniversityofNottingham,SuttonBoningtonCampus,
Loughborough,Leicestershire,LE125RD,UK;
DrDavidEvans,SchoolofBiologicalandMolecularSciences,Oxford
BrookesUniversity,Headington,Oxford,OX30BP;
DrMichaelT.McManus,InstituteofMolecularBioSciences,Massey
University,PalmerstonNorth,NewZealand;
DrJocelynK.C.Rose,DepartmentofPlantBiology,CornellUniversity,
Ithaca,NewYork14853,USA.
Titlesintheseries:
1. Arabidopsis
EditedbyM.AndersonandJ.A.Roberts
2. BiochemistryofPlantSecondaryMetabolism
EditedbyM.Wink
3. FunctionsofPlantSecondaryMetabolitesandtheirExploitationin
Biotechnology
EditedbyM.Wink
4. MolecularPlantPathology
EditedbyM.DickinsonandJ.Beynon
5. VacuolarCompartments
EditedbyD.G.RobinsonandJ.C.Rogers
6. PlantReproduction
EditedbyS.D.O’NeillandJ.A.Roberts
7. Protein–ProteinInteractionsinPlantBiology
EditedbyM.T.McManus,W.A.Laing,andA.C.Allan
8. ThePlantCellWall
EditedbyJ.K.C.Rose
9. TheGolgiApparatusandthePlantSecretoryPathway
EditedbyD.G.Robinson
10. ThePlantCytoskeletoninCellDifferentiationandDevelopment
EditedbyP.J.Hussey
11. Plant–PathogenInteractions
EditedbyN.J.Talbot
12. PolarityinPlants
EditedbyK.Lindsey
13. Plastids
EditedbyS.G.Moller
14. PlantPigmentsandtheirManipulation
EditedbyK.M.Davies
15. MembraneTransportinPlants
EditedbyM.R.Blatt
16. IntercellularCommunicationinPlants
EditedbyA.J.Fleming
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17. PlantArchitectureandItsManipulation
EditedbyC.G.N.Turnbull
18. Plasmodeomata
EditedbyK.J.Oparka
19. PlantEpigenetics
EditedbyP.Meyer
20. FloweringandItsManipulation
EditedbyC.Ainsworth
21. EndogenousPlantRhythms
EditedbyA.HallandH.McWatters
22. ControlofPrimaryMetabolisminPlants
EditedbyW.C.PlaxtonandM.T.McManus
23. BiologyofthePlantCuticle
EditedbyM.Riederer
24. PlantHormoneSignaling
EditedbyP.HaddenandS.G.Thomas
25. PlantCellSeparationandAdhesion
EditedbyJ.R.RobertsandZ.Gonzalez-Carranza
26. SenescenceProcessesinPlants
EditedbyS.Gan
27. SeedDevelopment,DormancyandGermination
EditedbyK.J.BradfordandH.Nonogaki
28. PlantProteomics
EditedbyC.Finnie
29. RegulationofTranscriptioninPlants
EditedbyK.Grasser
30. LightandPlantDevelopment
EditedbyG.Whitelam
31. PlantMitochondria
EditedbyD.C.Logan
32. CellCycleControlandPlantDevelopment
EditedbyD.Inze´
33. IntracellularSignalinginPlants
EditedbyZ.Yang
34. MolecularAspectsofPlantDiseaseResistance
EditedbyJ.Parker
35. PlantSystemsBiology
EditedbyG.M.CoruzziandR.A.Gutie´rrez
36. TheMossPhyscomitrellapatens
EditedbyC.D.Knight,P.-F.PerroudandD.J.Cove
37. RootDevelopment
EditedbyT.Beeckman
38. FruitDevelopmentandSeedDispersal
EditedbyLarsØstergaard
39. FunctionsandBiotechnologyofPlantSecondaryMetabolites
EditedbyM.Wink
40. BiochemistryofPlantSecondaryMetabolism
EditedbyM.Wink
41. PlantPolysaccharides
EditedbyP.Ulvskov
42. NitrogenMetabolisminPlantsinthePost-genomicEra
EditedbyC.FoyerandH.Zhang
43. BiologyofPlantMetabolomics
EditedbyR.D.Hall
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CONTENTS
Contributors xv
Preface xxiii
Acknowledgements xxv
1 PlantMetabolomicsinaNutshell:PotentialandFutureChallenges 1
RobertD.Hall
1.1 Thehistoryandthegoalsofplantmetabolomics 1
1.2 Thetechnologies 4
1.2.1 Extraction,separationanddetection 6
1.2.2 Datageneration,storage,processingandmining 7
1.3 Theapplications 10
1.3.1 Metabolomicsandfundamentalplantresearch 11
1.3.2 Metabolomicsandappliedplantresearch 13
1.4 Thebottlenecks,thepotentialandfuturechallenges 15
1.4.1 Currentlimitations 16
1.4.2 Futurepotential 18
1.4.3 Challengesforthefuture 19
Acknowledgements 20
References 20
2 MetaboliteAnalysisandMetabolomicsintheStudyof
BiotrophicInteractionsbetweenPlantsandMicrobes 25
JohnDraper,SusanneRasmussenandHassanZubair
2.1 Introduction 26
2.2 Biotrophicphasesofinteractionsbetweenfungal
pathogensandplanthosts 28
2.2.1 Hemi-biotrophicinteractionsbetween
Magnaporthegriseaandgrasshosts 29
2.2.2 Infectionofcerealhostsbytheobligate
pathogenBlumeriagraminis 33
2.2.3 Interactionsbetweenmaizeandsmut
pathogenUstilagomaydis 34
2.3 Mutualisticplantassociationswithendosymbionts 36
2.3.1 Legume–rhizobiumassociations 37
2.3.2 Plantroot–arbuscularmycorrhizalassociations 40
2.3.3 Neotyphodium–grassassociations 43
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viii (cid:1) Contents
2.4 Conclusions,horizonscanning&futureimpact 45
2.4.1 Commonaspectsofbiotrophicinteractions
derivedfrommetaboliteanalyses 46
2.4.2 Technicalchallengesremaininginthestudy
ofbiotrophicinteractions 47
References 49
3 AbioticStressandMetabolomics 61
JairusBowne,AntonyBacic,MarkTesterandUteRoessner
3.1 Introduction 61
3.2 Whatisabioticstressandhowdoesitimpactcrop
production? 63
3.3 Abioticstressadaptationandtolerancemechanisms:
molecularandphysiologicalapproaches 64
3.4 Metabolomics 65
3.4.1 Gaschromatography–massspectrometry 66
3.4.2 Liquidchromatography–massspectrometry 68
3.4.3 Capillaryelectrophoresis–massspectrometry 69
3.4.4 Nuclearmagneticresonance 69
3.5 Impactofabioticstressonplantmetabolism 70
3.5.1 Drought 71
3.5.2 Coldstress 72
3.5.3 Salinity 73
3.6 Integrationof‘omicsandphysiologicaldata 74
3.7 Howcantechnologicalimprovementsassistindata
interpretation? 75
3.8 Wheredowegofromhere? 76
References 77
4 ARoleforMetabolomicsinPlantEcology 87
NicoleM.vanDamandEddyvanderMeijden
4.1 Aplantisneveralone 88
4.2 Applyingmetabolomicstowildplantspecies:yes
wecan! 89
4.3 Plantmetabolomicsandchemicalecologyof
plant–insectinteractions:somesuccessstories 92
4.3.1 Thechemicalconsequencesofhybridization
inplants 92
4.3.2 Thesearchforresistancetraits 93
4.3.3 Genotypexenvironmentinteractionsin
plantchemistry 94
4.4 Plantmetabolomicshelpstoadvancetheoriesinplant
insectinteractions 96
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Contents (cid:1) ix
4.4.1 Optimaldefencetheories:unravelling
differentplantdefencestrategies 96
4.4.2 Testingtheoriesofinvasiveplantspeciesbiology 99
4.5 Metabolomicsforplantecologyinthefuture:
possibilitiesandpitfalls 101
References 102
5 MetabolomicsofaModelFruit:Tomato 109
RicC.H.deVos,RobertD.HallandAnnickMoing
5.1 Introduction 110
5.1.1 Tomatoasamodelforfleshyfruit 110
5.1.2 Metabolomicstechniquesintomatofruitresearch 111
5.1.3 Tomatometabolitedatabases 118
5.2 Afewkeyexamplesofthebroadrelevanceoftomato
fruitmetabolomics 120
5.2.1 Tomatometabolomicsandhumannutrition 120
5.2.2 Metabolomicsforqualitydiagnosticsof
tomatofruitandtheirproducts 127
5.2.3 Geneticalmetabolomicsintomato 130
5.2.4 Tomatometabolomicsandfunctional
genomicsstudies 132
5.3 Predictionsforthefuture 137
5.3.1 Highthroughputstrategies 137
5.3.2 Micrometabolomics,metabolite
compartmentationandimaging 139
5.3.3 Metaboliteidentificationanddatabases 140
5.3.4 Dataintegrationbetweenmetabolomics
platformsandbetweenomicsstrategies 142
5.4 Conclusions 143
Acknowledgements 144
References 144
6 MetabolomicsofArabidopsisthaliana 157
MichaelH.BealeandMichaelR.Sussman
6.1 Introduction 157
6.2 TheArabidopsismetabolome 159
6.3 MeasuringtheArabidopsismetabolome 162
6.3.1 Technologyandmethodology 163
6.3.2 Puttingthetechnologyintopractice:targeted
vs.untargetedmetabolomics 166
6.4 MetabolomicsandArabidopsismolecularplantphysiology 168
6.5 MetabolomicsinArabidopsisfunctionalgenomics 170
6.6 Geneticalmetabolomics 172
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x (cid:1) Contents
6.7 Forwardlook 173
Acknowledgements 174
References 174
7 CropsandTasty,NutritiousFood–HowCanMetabolomicsHelp? 181
DerekStewart,LouiseV.T.Shepherd,RobertD.HallandPaulD.
Fraser
7.1 Everyfoodchainbeginswithplants 182
7.2 Potatoandtomato–bothfreshandprocessed 182
7.2.1 Potatometabolomics 183
7.2.2 Freshtomatoes 185
7.2.3 Tomatopuree–amodelforthefood
processingindustry? 187
7.3 Graincrops 188
7.3.1 Thecereals 188
7.3.2 Ricemetabolomics 190
7.4 Softfruitmetabolomics 192
7.5 Metabolomicsandourmostimportantbeverages–
coffee,teaandwine 194
7.5.1 Coffeemetabolomics 194
7.5.2 Teametabolomics 196
7.5.3 Grapesandwine 198
7.6 Foodproductcontaminationandadulteration 200
7.7 Metaboliteprofilingtechnologiesusedtoevaluate
cropsafety 201
7.7.1 Thegenerationandstandardizationofthe
biologicalmaterial 201
7.7.2 Evaluationofnovelfoodstuffsusingtargeted
metaboliteprofiling 202
7.7.3 Evaluationofnovelfoodstuffsusing
metabolomicandchemicalfingerprinting 203
7.7.4 Metabolomicsinthedevelopmentand
evaluationofGMcrops 205
7.7.5 Non-targetedapproachesanddetectionof
unintendedeffects 206
7.8 Thefutureimportanceofmetabolomicsincropresearch 206
Acknowledgements 208
References 208
8 Genetics,GenomicsandMetabolomics 219
AlisdairR.FernieandJoostJ.B.Keurentjes
8.1 Introduction 220
8.2 Geneticunderstandingofmetabolisminthe
pre-genomicsera 221