mRNA穩(wěn)定性和細(xì)胞內(nèi)定位

Chapter22

mRNAStabilityandLocalization22.1Introduction3′UTR

(3′untranslatedregion)–TheuntranslatedsequencedownstreamfromthecodingregionofanmRNA.5′UTR

(5′untranslatedregion)–TheuntranslatedsequenceupstreamfromthecodingregionofanmRNA.FIGURE01:FeaturesofprokaryoticandeukaryoticmRNAs.22.1Introductionstem-loop–AsecondarystructurethatappearsinRNAsconsistingofabase-pairedregion(stem)andaterminalloopofsingle-strandedRNA.Botharevariableinsize.22.2MessengerRNAsAreUnstableMoleculesmRNAinstabilityisduetotheactionofribonucleases.Ribonucleasesdifferintheirsubstratepreferenceandmodeofattack.endoribonuclease–AribonucleasethatcleavesanRNAataninternalsite(s).exoribonuclease–AribonucleasethatremovesterminalribonucleotidesfromRNA.FIGURE02:Typesofribonucleases.22.2MessengerRNAsAreUnstableMoleculesprocessive(nuclease)–Anenzymethatremainsassociatedwiththesubstratewhilecatalyzingthesequentialremovalofnucleotides.distributive(nuclease)–Anenzymethatcatalyzestheremovalofonlyoneorafewnucleotidesbeforedissociatingfromthesubstrate.mRNAsexhibitawiderangeofhalf-lives.FIGURE03:MethodfordeterminingmRNAhalf-lives.22.2MessengerRNAsAreUnstableMoleculesmRNAdecay–mRNAdegradation,assumingthatthedegradationprocessisstochastic(隨機(jī)的).DifferentialmRNAstabilityisanimportantcontributortomRNAabundanceandthereforethespectrumofproteinsmadeinacell.steadystate(molecularconcentration)–Theconcentrationofpopulationofmoleculeswhentheratesofsynthesisanddegradationareconstant.22.3EukaryoticmRNAsExistintheFormofmRNPsfromTheirBirthtoTheirDeathmRNAassociateswithachangingpopulationofproteinsduringitsnuclearmaturationandcytoplasmiclife.Somenuclear-acquiredmRNPproteinshaverolesinthecytoplasm.AverylargenumberofRNA-bindingproteins(RBPs)exist,mostofwhichremainuncharacterized.DifferentmRNAsareassociatedwithdistinct,butoverlapping,setsofregulatoryproteins,creatingRNAregulons.FIGURE04:TheconceptofanRNAregulon.22.4ProkaryoticmRNADegradationInvolvesMultipleEnzymespolyribosome(orpolysome)–AnmRNAthatissimultaneouslybeingtranslatedbymultipleribosomes.monocistronicmRNA–mRNAthatcodesforonepolypeptide.22.4ProkaryoticmRNADegradationInvolvesMultipleEnzymesDegradationofbacterialmRNAsisinitiatedbyremovalofapyrophosphatefromthe5′terminus.MonophosphorylatedmRNAsaredegradedduringtranslationinatwo-stepcycleinvolvingendonucleolyticcleavages,followedby3′to5′digestionoftheresultingfragments.FIGURE05:DegradationofbacterialmRNAs22.4ProkaryoticmRNADegradationInvolvesMultipleEnzymes3′polyadenylationcanfacilitatethedegradationofmRNAfragmentscontainingsecondarystructure.poly(A)

polymerase(PAP)–Theenzymethataddsthestretchofpolyadenylicacidtothe3′endofeukaryoticmRNA.Itdoesnotuseatemplate.22.4ProkaryoticmRNADegradationInvolvesMultipleEnzymespoly(A)–Astretchofadenylicacidthatisaddedtothe3′endofmRNAfollowingitssynthesis.Themaindegradationenzymesworkasacomplexcalledthedegradosome.

22.5MostEukaryoticmRNAisDegradedviaTwoDeadenylation-DependentPathwaysThemodificationsatbothendsofmRNAprotectitagainstdegradationbyexonucleases.poly(A)

bindingprotein(PABP)–Theproteinthatbindstothe3′stretchofpoly(A)onaeukaryoticmRNA.22.5MostEukaryoticmRNAisDegradedviaTwoDeadenylation-DependentPathwaysThetwomajormRNAdecaypathwaysareinitiatedbydeadenylationcatalyzedbypoly(A)nucleases.Deadenylationmaybefollowedeitherbydecappingand5′to3′exonucleasedigestion,orby3′to5′exonucleasedigestion.FIGURE06:Themajordeadenylation-dependentdecaypathwaysineukaryotes22.5MostEukaryoticmRNAisDegradedviaTwoDeadenylation-DependentPathwaysThedecapping

enzymecompeteswiththetranslationinitiationcomplexfor5′capbinding.cytoplasmiccap-bindingprotein–Acomponentoftheeukaryoticinitiationfactor4F(eIF4F)thatbindsthe7-methylguanosinecapatthe5′endofeukaryoticmRNA.Theexosome,whichcatalyzes3′to5′mRNAdigestion,isalarge,evolutionarilyconservedcomplex.22.5MostEukaryoticmRNAisDegradedviaTwoDeadenylation-DependentPathwaysDegradationmayoccurwithindiscretecytoplasmicparticlescalledprocessingbodies(PBs).AvarietyofparticlescontainingtranslationallyrepressedmRNAsexistindifferentcelltypes.maternalmRNAgranules–OocyteparticlescontainingtranslationallyrepressedmRNAsawaitingactivationlaterindevelopment.22.5MostEukaryoticmRNAisDegradedviaTwoDeadenylation-DependentPathwaysneuronalgranules–ParticlescontainingtranslationallyrepressedmRNAsintransittofinalcelldestinations.stressgranules–Cytoplasmicparticles,containingtranslationallyinactivemRNAs,thatforminresponsetoageneralinhibitionoftranslationinitiation.22.6OtherDegradationPathwaysTargetSpecificmRNAsFouradditionaldegradationpathwaysinvolveregulateddegradationofspecificmRNAs.Deadenylation-independentdecappingproceedsinthepresenceofalongpoly(A)tail.FIGURE08:Otherdecaypathwaysineukaryoticcells22.6OtherDegradationPathwaysTargetSpecificmRNAsThedegradationofthenonpolyadenylatedhistonemRNAsisinitiatedby3′additionofapoly(U)tail.DegradationofsomemRNAsmaybeinitiatedbysequence-specificorstructure-specificendonucleolyticcleavage.AnunknownnumberofmRNAsaretargetsfordegradationortranslationalrepressionbymicroRNAs.22.6OtherDegradationPathwaysTargetSpecificmRNAsFIGURE09:TablesummarizingkeyelementsofmRNAdecaypathwaysineukaryoticcells22.7mRNA-SpecificHalf-LivesAreControlledbySequencesorStructureswithinthemRNASpecificcis-elementsinanmRNAaffectitsrateofdegradation.Destabilizingelements(DEs)canacceleratemRNAdecay,whilestabilizingelements(SEs)canreduceit.FIGURE10:Mechanismsbywhichdestabilizingelements(DEs)andstabilizingelements(SEs)function22.7mRNA-SpecificHalf-LivesAreControlledbySequencesorStructureswithinthemRNAAU-richelements(AREs)arecommondestabilizingelementsinmammals,andareboundbyavarietyofproteins.SomeDE-bindingproteinsinteractwithcomponentsofthedecaymachineryandprobablyrecruitthemfordegradation.StabilizingelementsoccuronsomehighlystablemRNAs.22.7mRNA-SpecificHalf-LivesAreControlledbySequencesorStructureswithinthemRNAmRNAdegradationratescanbealteredinresponsetoavarietyofsignals.iron-responseelement(IRE)–AcissequencefoundincertainmRNAswhosestabilityortranslationisregulatedbycellularironconcentration.FIGURE11:RegulationoftransferringmRNAstabilitybyironlevels22.8NewlySynthesizedRNAsAreCheckedforDefectsviaaNuclearSurveillanceSystemAberrantnuclearRNAsareidentifiedanddestroyedbyanRNAsurveillancesystem.ThenuclearexosomefunctionsbothintheprocessingofnormalsubstrateRNAsandinthedestructionofaberrantRNAs.TheyeastTRAMPcomplexrecruitstheexosometoaberrantRNAsandfacilitatesits3′to5′exonucleaseactivity.22.8NewlySynthesizedRNAsAreCheckedforDefectsviaaNuclearSurveillanceSystemoligo(A)tail–ashortpoly(A)tail,generallyreferringtoastretchoflessthan15adenylates.SubstratesforTRAMP-exosomedegradationincludeunsplicedoraberrantlysplicedpre-mRNAsandimproperlyterminatedRNAPolIItranscriptslackingapoly(A)tail.FIGURE12:TheroleofTRAMPandtheexosomeindegradingaberrantnuclearRNAs22.8NewlySynthesizedRNAsAreCheckedforDefectsviaaNuclearSurveillanceSystemThemajorityofRNAPolIItranscriptsmaybecrypticunstabletranscripts(CUTs)thatarerapidlydestroyedinthenucleus.22.9QualityControlofmRNATranslationIsPerformedbyCytoplasmicSurveillanceSystemsreleasefactor(RF)–AproteinrequiredtoterminatepolypeptidetranslationtocausereleaseofthecompletedpolypeptidechainandtheribosomefrommRNA.Nonsense-mediateddecay(NMD)targetsmRNAswithprematurestopcodons.TargetingofNMDsubstratesrequiresaconservedsetofUpfandSMGproteins.22.9QualityControlofmRNATranslationIsPerformedbyCytoplasmicSurveillanceSystemsRecognitionofaterminationcodonasprematureinvolvesunusual3′UTRstructureorlengthinmanyorganismsandthepresenceofdownstreamexonjunctioncomplexes(EJC)inmammals.pioneerroundoftranslation–ThefirsttranslationeventforanewlysynthesizedandexportedmRNA.FIGURE14:Twomechanismsbywhichaterminationcodonisrecognizedaspremature22.9QualityControlofmRNATranslationIsPerformedbyCytoplasmicSurveillanceSystemsNonstopdecay(NSD)targetsmRNAslackinganin-frameterminationcod