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Metabolome: From Wikipedia, The Free Encyclopedia
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ofsmallmoleculechemicalsfoundwithina
biologicalsample.[1]Thebiologicalsample
Mainpage
canbeacell,acellularorganelle,anorgan,
Contents
atissue,atissueextract,abiofluidoran
Featuredcontent
entireorganism.Thesmall
Currentevents
moleculechemicalsfoundinagiven
Randomarticle
metabolomemayincludeboth
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endogenousmetabolitesthatarenaturally
producedbyanorganism(suchasamino
acids,organicacids,nucleicacids,fatty
Figure1.Anillustrationofthe
pyramidoflifewhichshowsthe
varyinginfluenceoftheenvironment
andphysiologyonthegenome,
proteomeandmetabolome.
acids,amines,sugars,vitamins,co
Communityportal
factors,pigments,antibiotics,etc.)aswellasexogenouschemicals(suchas
Recentchanges
drugs,environmentalcontaminants,foodadditives,toxinsandotherxenobiotics)
Contactpage
thatarenotnaturallyproducedbyanorganism.[2][3]Inotherwords,thereisbothan
endogenousmetabolomeandanexogenousmetabolome.Theendogenous
Tools
Whatlinkshere
metabolomecanbefurthersubdividedtoincludea"primary"anda"secondary"
Relatedchanges
metabolome(particularlywhenreferringtoplantormicrobialmetabolomes).
Uploadfile
Aprimarymetaboliteisdirectlyinvolvedinthenormalgrowth,development,and
Specialpages
reproduction.Asecondarymetaboliteisnotdirectlyinvolvedinthoseprocesses,but
Permanentlink
Pageinformation
Wikidataitem
Citethispage
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Createabook
usuallyhasimportantecologicalfunction.Secondarymetabolitesmay
includepigments,antibioticsorwasteproductsderivedfrompartially
metabolizedxenobiotics.Toqualifyasametabolite,ortobeconsideredtobepartof
themetabolome,asmallmoleculemusttypicallyhaveamolecularweight<1500
Da.[2]Thismeansthatmoleculessuchasglycolipids,polysaccharides,
DownloadasPDF
shortpeptides(<14aminoacids)andsmalloligonucleotides(<5bases)canbe
Printableversion
regardedasmetabolitesorconstituentsofthemetabolome.Ontheotherhand,
Languages
verylargemacromoleculessuchasproteins,messengerRNA,ribosomal
Bosanski
RNA,microRNAandDNAaredefinitelynotmetabolitesandarenotconsideredto
Catal
bepartofthemetabolome.Thestudyofthemetabolomeiscalledmetabolomics.
Deutsch
SeeFigure1forapictureoftherelationshipbetweendifferentomes.
Espaol
Contents[hide]
Franais
Galego
BahasaIndonesia
Italiano
Magyar
Nederlands
https://en.wikipedia.org/wiki/Metabolome
1 Origins
2 Measuringthemetabolome
3 Metabolomedatabases
3.1 TheHumanMetabolomeDatabase
3.1.1 Humanbiofluidmetabolomes
3.2 YeastMetabolomeDatabase
Figure2.Anillustrationofthe
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Polski
relationshipbetweensensitivity(or
lowerdetectionlimitinconcentration
units)andthenumberofmetabolites
detected(usingaLog10scale)via
differentmetabolomicstechnologies.
3.3 TheEscherichiacoliMetabolome
Database
/srpski
Srpskohrvatski/
4 Seealso
5 References
6 Externallinks
Svenska
TingVit
Editlinks
Origins
[ edit ]
Thewordmetabolomeappearstobeablendingofthewordsmetaboliteand
chromosome.Itwasconstructedtoimplythatmetabolitesareindirectlyencoded
bygenesoractongenesandgeneproducts.Thetermmetabolomewasfirst
usedin1998[1][4]andwaslikelycoinedtomatchwithexistingbiologicalterms
referringtothecompletesetofgenes(thegenome),thecompletesetofproteins
(theproteome)andthecompletesetoftranscripts(thetranscriptome).Thefirst
bookonmetabolomicswaspublishedin2003.[5]Thefirstjournaldedicatedto
metabolomics(titledsimplyMetabolomics)waslaunchedin2005andiscurrently
editedbyDr.RoystonGoodacre.Someofthemoresignificantearlypaperson
metabolomeanalysisarelistedinthereferencesbelow[6][7][8][9]
Measuringthemetabolome
[ edit ]
Themetabolomereflectstheinteractionbetweenanorganismsgenomeandits
environment.Asaresult,anorganismsmetabolomecanserveasanexcellent
probeofitsphenotype(i.e.theproductofitsgenotypeandits
environment).Metabolitescanbemeasured(identified,quantifiedorclassified)
usinganumberofdifferenttechnologiesincludingNMRspectroscopyandmass
spectrometry.Mostmassspectrometry(MS)methodsmustbecoupledtovarious
formsofliquidchromatography(LC),gaschromatography(GC)orcapillary
electrophoresis(CE)tofacilitatecompoundseparation.Eachmethodistypically
abletoidentifyorcharacterize505000differentmetabolitesormetabolite
featuresatatime,dependingontheinstrumentorprotocolbeingused.See
Figure2foranillustrationoftherelationshipbetweendifferentanalyticalmethods
andtheirsensitivity.Currentlyitisnotpossibletoanalyzetheentirerangeof
metabolitesbyasingleanalyticalmethod.
Nuclearmagneticresonance(NMR)spectroscopyisananalyticalchemistry
techniquethatmeasurestheabsorptionofradiofrequencyradiationofspecificnuclei
whenmoleculescontainingthosenucleiareplacedinstrongmagneticfields.The
frequency(i.e.thechemicalshift)atwhichagivenatomornucleusabsorbsis
highlydependentonthechemicalenvironment(bonding,chemicalstructure
nearestneighbours,solvent)ofthatatominagivenmolecule.TheNMRabsorption
patternsproduceresonancepeaksatdifferentfrequenciesordifferentchemical
shiftsthiscollectionofpeaksiscalledaNMRspectrum.Becauseeachchemical
compoundhasadifferentchemicalstructure,eachcompoundwillhaveaunique
(oralmostunique)NMRspectrum.Asaresult,NMRisparticularlyusefulforthe
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characterization,identificationandquantificationofsmallmolecules,suchas
metabolites.ThewidespreaduseofNMRforclassicalmetabolicstudies,along
withitsexceptionalcapacitytohandlecomplexmetabolitemixturesislikelythe
reasonwhyNMRwasoneofthefirsttechnologiestobewidelyadoptedforroutine
metabolomemeasurements.Asananalyticaltechnique,NMRisnondestructive,
nonbiased,easilyquantifiable,requireslittleornoseparation,permitsthe
identificationofnovelcompoundsanditneedsnochemicalderivatization.NMRis
particularlyamenabletodetectingcompoundsthatarelesstractabletoLC
MSanalysis,suchassugars,aminesorvolatileliquidsorGCMSanalysis,suchas
largemolecules(>500Da)orrelativelynonreactivecompounds.NMRisnotavery
sensitivetechniquewithalowerlimitofdetectionofabout5M.Typically50150
compoundscanbeidentifiedbyNMRbasedmetabolomicstudies.
Massspectrometryisananalyticaltechniquethatmeasuresthemasstocharge
ratioofmolecules.Moleculesormolecularfragmentsaretypicallychargedor
ionizedbysprayingthemthroughachargedfield(electrosprayionization),
bombardingthemwithelectronsfromahotfilament(electronionization)orblasting
themwithalaserwhentheyareplacedonspeciallycoatedplates(matrixassisted
laserdesorptionionization).Thechargedmoleculesarethenpropelledthrough
spaceusingelectrodesormagnetsandtheirspeed,rateofcurvature,orother
physicalcharacteristicsaremeasuredtodeterminetheirmasstochargeratio.
Fromthesedatathemassoftheparentmoleculecanbedetermined.Further
fragmentationofthemoleculethroughcontrolledcollisionswithgasmoleculesor
withelectronscanhelpdeterminethestructureofmolecules.Veryaccuratemass
measurementscanalsobeusedtodeterminetheelementalformulasorelemental
compositionofcompounds.Mostformsofmassspectrometryrequiresomeformof
separationusingliquidchromatographyorgaschromatography.Thisseparation
stepisrequiredtosimplifytheresultingmassspectraandtopermitmoreaccurate
compoundidentification.Somemassspectrometrymethodsalsorequirethatthe
moleculesbederivatizedorchemicallymodifiedsothattheyaremoreamenable
forchromatographicseparation(thisisparticularlytrueforGCMS).Asananalytical
technique,MSisaverysensitivemethodthatrequiresverylittlesample(<1ngof
materialor<10Lofabiofluid)andcangeneratesignalsfor1000sofmetabolites
fromasinglesample.MSinstrumentscanalsobeconfiguredforveryhigh
throughputmetabolomeanalyses(100sto1000sofsamplesaday).Quantification
ofmetabolitesandthecharacterizationofnovelcompoundstructuresismore
difficultbyMSthanbyNMR.LCMSisparticularlyamenabletodetecting
hydrophobicmolecules(lipids,fattyacids)andpeptideswhileGCMSisbestfor
detectingsmallmolecules(<500Da)andhighlyvolatilecompounds
(esters,amines,ketones,alkanes,thiols).
Unlikethegenomeoreventheproteome,themetabolomeisahighlydynamic
entitythatcanchangedramatically,overaperiodofjustsecondsorminutes.Asa
result,thereisgrowinginterestinmeasuringmetabolitesovermultipletimeperiods
orovershorttimeintervalsusingmodifiedversionsofNMRorMSbased
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metabolomics
Metabolomedatabases
[ edit ]
Becauseanorganismsmetabolomeislargelydefinedbyitsgenome,different
specieswillhavedifferentmetabolomes.Indeed,thefactthatthemetabolomeofa
tomatoisdifferentthanthemetabolomeofanappleisthereasonwhythesetwo
fruitstastesodifferent.Furthermore,differenttissues,
differentorgansandbiofluidsassociatedwiththoseorgansandtissuescanalso
havedistinctlydifferentmetabolomes.Thefactthatdifferentorganismsand
differenttissues/biofluidshavesuchdifferentmetabolomeshasledtothe
developmentofanumberoforganismspecificofbiofluidspecificmetabolome
databases.SomeofthebetterknownmetabolomedatabasesincludetheHuman
MetabolomeDatabaseorHMDB,[10]theYeastMetabolome
DatabaseorYMDB,[11]theE.coliMetabolomeDatabaseorECMDB,[12]the
ArabidopsismetabolomedatabaseorAraCyc[13]aswellastheUrineMetabolome
Database,[14]theCerebrospinalFluid(CSF)MetabolomeDatabase[15]andthe
SerumMetabolomeDatabase.[16]Thelatterthreedatabasesarespecifictohuman
biofluids.Anumberofverypopulargeneralmetabolitedatabasesalsoexist
includingKEGG,[17]MetaboLights,[18]theGolmMetabolome
Database,[19]MetaCyc,[20]LipidMaps[21]andMetlin.[22]Metabolomedatabasescan
bedistinguishedfrommetabolitedatabasesinthatmetabolitedatabasescontain
lightlyannotatedorsynopticmetabolitedatafrommultipleorganismswhile
metabolomedatabasescontainrichlydetailedandheavilyreferencedchemical,
pathway,spectralandmetaboliteconcentrationdataforspecificorganisms.
TheHumanMetabolomeDatabase
[ edit ]
TheHumanMetabolomeDatabaseisafreelyavailable,openaccessdatabase
containingdetaileddataonmorethan40,000metabolitesthathavealreadybeen
identifiedorarelikelytobefoundinthehumanbody.TheHMDBcontainsthree
kindsofinformation:1)chemicalinformation,2)clinicalinformation,and3)
biochemicalinformation.Thechemicaldataincludes>40,000metabolitestructures
withdetaileddescriptions,extensivechemicalclassifications,synthesisinformation
andobserved/calculatedchemicalproperties.Italsocontainsnearly10,000
experimentallymeasuredNMR,GCMSandLC/MSspectrafrommorethan1100
differentmetabolites.Theclinicalinformationincludesdataon>10,000metabolite
biofluidconcentrations,metaboliteconcentrationinformationonmorethan600
differenthumandiseasesandpathwaydataformorethan200differentinborn
errorsofmetabolism.Thebiochemicalinformationincludesnearly6000protein
(andDNA)sequencesandmorethan5000biochemicalreactionsthatarelinkedto
thesemetaboliteentries.TheHMDBsupportsawidevarietyofonlinequeries
includingtextsearches,chemicalstructuresearches,sequencesimilaritysearches
andspectralsimilaritysearches.Thismakesitparticularlyusefulformetabolomic
researcherswhoareattemptingtoidentifyorunderstandmetabolitesinclinical
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metabolomicstudies.ThefirstversionoftheHMDBwasreleasedinJan.12007
andwascompiledbyscientistsattheUniversityofAlbertaandtheUniversityof
Calgary.Atthattimetheyreporteddataon2,500metabolites,1,200drugsand
3,500foodcomponents.Sincethenthesescientistshavegreatlyexpandedthe
collection.ThelatestversionoftheHMDB(version3.5)contains>16,000
endogenousmetabolites,>1500drugsand>22,000foodconstituentsorfood
metabolites.[23]
Humanbiofluidmetabolomes [ edit ]
ScientistsattheUniversityofAlbertahavebeensystematicallycharacterizing
specificbiofluidmetabolomesincludingtheserummetabolome,[16]theurine
metabolome,[14]thecerebrospinalfluid(CSF)metabolome[15]andthesaliva
metabolome.Theseeffortshaveinvolvedbothexperimentalmetabolomicanalysis
(involvingNMR,GCMS,ICPMS,LCMSandHPLCassays)aswellasextensive
literaturemining.Accordingtotheirdata,thehumanserummetabolomecontainsat
least4200differentcompounds(includingmanylipids),thehumanurine
metabolomecontainsatleast3000differentcompounds(including100sofvolatiles
andgutmicrobialmetabolites),thehumanCSFmetabolomecontainsnearly500
differentcompoundswhilethehumansalivametabolomecontainsapproximately
400differentmetabolites,includingmanybacterialproducts.
YeastMetabolomeDatabase
[ edit ]
TheYeastMetabolomeDatabaseisafreelyaccessible,onlinedatabaseof>2000
smallmoleculemetabolitesfoundinorproducedbySaccharomyces
cerevisiae(Bakersyeast).TheYMDBcontainstwokindsofinformation:1)
chemicalinformationand2)biochemicalinformation.Thechemicalinformationin
YMDBincludes2027metabolitestructureswithdetailedmetabolitedescriptions,
extensivechemicalclassifications,synthesisinformationandobserved/calculated
chemicalproperties.Italsocontainsnearly4000NMR,GCMSandLC/MSspectra
obtainedfrommorethan500differentmetabolites.Thebiochemicalinformation
inYMDBincludes>1100protein(andDNA)sequencesand>900biochemical
reactions.TheYMDBsupportsawidevarietyofqueriesincludingtextsearches,
chemicalstructuresearches,sequencesimilaritysearchesandspectralsimilarity
searches.Thismakesitparticularlyusefulformetabolomicresearcherswhoare
studyingyeastasamodelorganismorwhoarelookingintooptimizingthe
productionoffermentedbeverages(wine,beer).
TheEscherichiacoliMetabolomeDatabase
[ edit ]
TheE.ColiMetabolomeDatabaseisafreelyaccessible,onlinedatabaseof>2700
smallmoleculemetabolitesfoundinorproducedbyEscherichiacoli(E.colistrain
K12,MG1655).TheECMDBcontainstwokindsofinformation:1)chemical
informationand2)biochemicalinformation.Thechemicalinformationincludes
morethan2700metabolitestructureswithdetailedmetabolitedescriptions,
extensivechemicalclassifications,synthesisinformationandobserved/calculated
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chemicalproperties.Italsocontainsnearly5000NMR,GCMSandLCMSspectra
frommorethan600differentmetabolites.Thebiochemicalinformationincludes
>1600protein(andDNA)sequencesand>3100biochemicalreactionsthatare
linkedtothesemetaboliteentries.TheECMDBsupportsmanydifferenttypesof
onlinequeriesincludingtextsearches,chemicalstructuresearches,sequence
similaritysearchesandspectralsimilaritysearches.Thismakesitparticularlyuseful
formetabolomicresearcherswhoarestudyingE.coliasamodelorganism.
Seealso
[ edit ]
Tumormetabolome
Metabolismportal
Proteinelectrophoresis
Proteinsequencing.
References
[ edit ]
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JW,GoodfriendT,WishartDS.(Feb2011)."Thehumanserummetabolome." .PLoS
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Externallinks
[ edit ]
Lookupmetabolomein
Wiktionary,thefree
dictionary.
Categories: Metabolism
Systemsbiology
Bioinformatics
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