Plant single cell and single cell type Metabolomics Review UF Download (1)

FeatureReview

Plantsingle-cellandsingle-cell-typemetabolomics

BiswapriyaB.Misra1,SarahM.Assmann2,andSixueChen1,3

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DepartmentofBiology,GeneticsInstitute,PlantMolecularandCellularBiologyProgram,UniversityofFlorida,Gainesville,FL32610,USA2

DepartmentofBiology,PennStateUniversity,208MuellerLaboratory,UniversityPark,PA16802,USA3

InterdisciplinaryCenterforBiotechnologyResearch,UniversityofFlorida,Gainesville,FL32610,USA

Inconjunctionwithgenomics,transcriptomics,andpro-teomics,plantmetabolomicsisprovidinglargedatasetsthatarepavingthewaytowardsacomprehensiveandholisticunderstandingofplantgrowth,development,defense,andproductivity.However,dilutioneffectsfromorgan-andtissue-basedsamplingofmetabolomeshavelimitedourunderstandingoftheintricateregula-tionofmetabolicpathwaysandnetworksatthecellularlevel.Recentadvancesinmetabolomicsmethodologies,alongwiththepost-genomicexpansionofbioinformat-icsknowledgeandfunctionalgenomicstools,haveallowedthegatheringofenrichedinformationonindi-vidualcellsandsinglecelltypes.Herewereviewprog-ress,currentstatus,opportunities,andchallengespresentedbysinglecell-basedmetabolomicsresearchinplants.

Metabolomicsatcellularresolution

Metabolitesaddanimportantextradimensiontotheinformation owfromDNAtoRNAtoprotein.Withtheadventofhigh-endinstrumentationandanacceleratedunderstandingoftherolesofmetabolitesinorganismalfunctions[1],ourappreciationoftheimportanceofmetab-olitesisincreasing.Byde nition,themetabolomeistheentiresetofsmallmolecules(molecularmasslessthan2,000Da)ormetabolitesinagivenbiologicalsample.Metabolomicsistheunbiasedanalyticalassessmentofthemetabolome,whereasmetabolite/metabolicpro lingdealswiththedetectionandquanti cationofagroupofmetabolitesusingaparticularanalyticalapproach[2].Thetotalnumberofmetabolitesfoundinplantsiscurrentlyestimatedat200,000,witharound7,000–15,000beingfoundinanyindividualspecies[3,4],3,000–5,000ofwhichresideinleaves[5,6].Theselargegroupsofstructurallydiverse,temporallyandspatiallydynamiccompoundsposegreatchallengesformodernanalyticaltechnologies[7]comparedwiththecomparativelystraightforwardpoly-mericassembliesoffournucleotidesasDNAmolecules.Inaddition,speciesspeci cityinthedistributionofspe-cializedmetabolites,rapidendogenousturnoverrates,an

Correspondingauthor:Chen,S.(schen@ufl.edu).

Keywords:metabolomics;massspectrometry;singlecell;singlecelltype;systems

Plant single cell and single cell type Metabolomics Review UF Download (1)

biology.

1360-1385/

ß2014ElsevierLtd.Allrightsreserved.http://www.wendangwang.com/10.1016/j.tplants.2014.05.005

inabilitytoamplifymetabolites,thelimitedabilitytocapturemorethanasnapshotofthemetabolitesinanorganismatanyonetime,thesuboptimalqualityofex-tractionmethods,andthedynamicrangesofabundance,detectioncapabilities,ionizationandpolarizabilityrendermetabolomicsfarmoredif cultthanother‘omics’.Itisnodoubtthatmetabolomicsstudiesareofessentialimpor-tanceforacomprehensiveunderstandingofcellularfunc-tions[8,9],andmetabolomicshasbecomeimportantinstudyingthegeneticregulationofmetabolitesynthesisandfunction[10].Large-scalediscoveryandquantitationofmetabolitesisimperativeforcomprehensiveunder-standingofplantsignalingandbiochemicalprocesses.Inaddition,manyphytochemicalshaveimmensesigni -canceinfood,medicine,andagriculture.

Alongsidetissue-,organ-,andorganism-levelmetabo-lomestudies,toolsandtechniqueshavebeendevelopedtoovercometheaveragingeffectthatisinevitableinstudiesonpopulationsofmixedcelltypes.Indeed,advancesintheisolationofbothsinglecellsandpopulationsofanindivid-ualcelltypehavemademetabolomicsatthecellularlevelareality,thusenhancingunbiaseddetectionandquanti ca-tionofmetabolitesatthisbasiclevelofbiologicalorgani-zation[11].Celltypeshavebeende nedonthebasisoftheirappearance,location,expressionofspeci cmarkergenes,orperformanceofspeci cfunctions[12].Todate,thechoiceofcellsystemstostudyhasbeendictatedlargelybytheeaseofisolation,handling,purityandhomogeneityofpreparations,stateofdifferentiation,andimportancetotheplant’sphysiologicalstatus.Here,wede nesingle-cellmetabolomesasthosederivedfromoneindividualcell(e.g.,asingleepidermalcell),whereassingle-cell-typemetabolomesarede nedasthosederivedfromapopula-tionofcellsrepresentingacommonoriginandphysiologi-calrole(e.g.,trichomesorguardcells).

Higherplantsaremulticellularorganisms:forexample,inrice40differentcelltypesaredocumented[13].Todate,enrichedorpurepreparationsofmanycelltypesfromdifferentplantspecieshavebeenusedforsingle-cellorsingle-cell-typemetabolomicsstudies(Table1,Figure1).Excellenttopicalreviewshaveappearedthatsummarizesubstantialprogressintheareasofsingle-cellgenomics[14],transcriptomics[15],andproteomics[16]ofplants.Inthisreview,wepresentrecentadvancesinplantsingle-cellandsingle-cell-typemetabolomics.Wehighlightthesam-plingtools,techniques,andvariousanalyticalplatforms,

TrendsinPlantSciencexx(2014)1–10

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