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The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses ... PDF

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RESEARCHARTICLE The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys LucieEtienne1*¤,FredericBibollet-Ruche2,PeterH.Sudmant3,LilyI.Wu1,Beatrice H.Hahn2,MichaelEmerman1* 1 DivisionsofHumanBiologyandBasicSciences,FredHutchinsonCancerResearchCenter,Seattle, Washington,UnitedStatesofAmerica,2 DepartmentsofMedicineandMicrobiology,PerelmanSchoolof Medicine,UniversityofPennsylvania,Philadelphia,Pennsylvania,UnitedStatesofAmerica,3 Department ofGenomeSciences,UniversityofWashingtonSchoolofMedicine,Seattle,Washington,UnitedStatesof America ¤ Currentaddress:CIRI,InternationalCenterforInfectiologyResearch,ENS-Lyon,UCBL,INSERMU1111, CNRSUMR5308,Lyon,France *[email protected](LE);[email protected](ME) Abstract OPENACCESS Citation:EtienneL,Bibollet-RucheF,SudmantPH, Cross-speciestransmissionsofvirusesfromanimalstohumansareattheoriginofmajor WuLI,HahnBH,EmermanM(2015)TheRoleofthe humanpathogenicviruses.Whiletheroleofecologicalandepidemiologicalfactorsinthe AntiviralAPOBEC3GeneFamilyinProtecting ChimpanzeesagainstLentivirusesfromMonkeys. emergenceofnewpathogensiswelldocumented,theimportanceofhostfactorsisoften PLoSPathog11(9):e1005149.doi:10.1371/journal. unknown.Chimpanzeesaretheclosestrelativesofhumansandtheanimalreservoiratthe ppat.1005149 originofthehumanAIDSpandemic.However,despitebeingregularlyexposedtomonkey Editor:ChristopherAiken,VanderbiltUniversity lentivirusesthroughhunting,chimpanzeesarenaturallyinfectedbyonlyasinglesimian SchoolofMedicine,UNITEDSTATES immunodeficiencyvirus,SIVcpz.Here,weaskedwhychimpanzeesappeartobeprotected Received:April22,2015 againstthesuccessfulemergenceofotherSIVs.Inparticular,weinvestigatedtheroleof Accepted:August13,2015 thechimpanzeeAPOBEC3genesinprovidingabarriertoinfectionbymostmonkeylentivi- ruses.WefoundthatmostSIVVifs,includingViffromSIVwrcinfectingwestern-redcolobus, Published:September22,2015 thechimpanzee’smainmonkeypreyinWestAfrica,couldnotantagonizechimpanzee Copyright:©2015Etienneetal.Thisisanopen APOBEC3G.Moreover,chimpanzeeAPOBEC3D,aswellasAPOBEC3FandAPO- accessarticledistributedunderthetermsofthe CreativeCommonsAttributionLicense,whichpermits BEC3H,providedadditionalprotectionagainstSIVVifantagonism.Consequently,lentiviral unrestricteduse,distribution,andreproductioninany replicationinprimarychimpanzeeCD4+Tcellswasdependentonthepresenceofalenti- medium,providedtheoriginalauthorandsourceare viralvifgenethatcouldantagonizechimpanzeeAPOBEC3s.Finally,byidentifyingand credited. functionallycharacterizingseveralAPOBEC3genepolymorphismsinbothcommonchim- DataAvailabilityStatement:Allrelevantdataare panzeesandbonobos,wefoundthattheseapepopulationsencodeAPOBEC3proteins withinthepaperanditsSupportingInformationfiles. thatareuniformlyresistanttoantagonismbymonkeylentiviruses. Funding:ThisworkwassupportedbyNIHgrants AI30937(toME),R37AI050529,R01AI058715,P30 AI045008(toBHH),YerkesBaseGrantORIP/OD P51OD011132forthechimpanzeeprimaycells,and anamfARMathildeKrimFellowshipinBasic AuthorSummary BiomedicalResearch(108499-53-RKGN,toLE).The fundershadnoroleinstudydesign,datacollection Manyhumanpathogensareofzoonoticorigin,meaningtheyoriginatedinanimals.This andanalysis,decisiontopublish,orpreparationof includesHIV-1,thecauseofthehumanAIDSpandemic,whichistheresultofcross- themanuscript. PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 1/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees CompetingInterests:Theauthorshavedeclared thatnocompetinginterestsexist. speciestransmissionsoflentivirusesfromchimpanzeesandgorillas.However,littleis knownaboutthehostfactorsthatprovidenaturalprotectionagainstviralemergenceina newspecies.Chimpanzees,whicharehumans’closestrelatives,harboronlyasinglelenti- virallineage,despitetheirfrequentexposuretolentivirusesthatinfectmonkeysonwhich theyprey.Here,weinvestigatethecapacityoftheaccessoryproteinViffromdifferentpri- matelentivirusestoantagonizetheAPOBEC3antiviralgenefamilyfoundinchimpanzees. WefoundthattheVifproteinfrommostmonkeylentiviruseswasnotabletoantagonize chimpanzeeAPOBEC3G.Furthermore,otherAPOBEC3proteinsfromchimpanzeeswere alsoresistanttoVifantagonism.Finally,weshowedthat,despitepolymorphisminthe APOBEC3genes,commonchimpanzeeandbonobopopulationsareuniformlyresistantto monkeylentiviralVifantagonism.Ourresultsareconsistentwiththehypothesisthatthe hostAPOBEC3antiviralproteinsprotectchimpanzeesagainstmanyHIV-relatedviruses commonlyfoundinmonkeys. Introduction AlthoughlentivirusesarewidespreadinAfricanmonkeys,therehaveonlybeenafewdocu- mentedcasesofcross-speciestransmissionandlentiviralemergenceintohominoids[1].Chim- panzeesareofparticularinterestbecausetheirlentivirus,SIVcpz,liesattherootofallHIV-1 infections[2].SIVcpzhasacomplexevolutionaryhistoryasitresultedfromthecross-species transmissionandrecombinationofSIVrcmfromred-cappedmangabeysandSIVmus/mon/ gsnfromguenons[3,4].However,onlycentralandeasternchimpanzeesareinfectedby SIVcpz,whilewesternandNigerian-Cameroonianchimpanzeesaswellasbonobosseemcur- rentlyfreeofanylentiviralinfection[1,5,6].Thefactthatchimpanzeesareinfectedbyonlya singlelentivirallineageissurprisinggiventhattheyareexposedtoSIVsthatarepresentathigh prevalenceintheirmonkeyprey[6,7].Moreover,therehavebeenmultipleviralcross-species transmissionsofsimianfoamyvirus(SFV)andsimianT-lymphotropicvirus(STLV)tochim- panzeesfromtheirmainprey,thewestern-redcolobus[8–10],yet,noinfectionwiththismon- keyspecies’lentivirus,SIVwrc,hasbeendocumentedinchimpanzees[6,7].Overall,this suggeststhattherearehostfactors,ratherthansolelyepidemiologicalorecologicalbarriers, thatprotectchimpanzeesagainsttheemergenceofnewlentiviralinfections. TherehavebeenfourindependenttransmissionsofHIV-1intohumansthatoriginated fromSIVcpz;twoofthesetransmissionshadtheirimmediatesourceinchimpanzees(HIV-1 groupsMandN),whiletwootherspassedthroughgorillasbeforeinfectinghumans(HIV-1 groupsOandP)[2,11].HIV-2,ontheotherhand,istheresultofcross-speciestransmissions ofSIVsmmfromsootymangabeystohumans[2].WhileSIVsmmhasjumpedtohumanson overnineindependentoccasions,neithertheequivalentSIVsmminfectionofchimpanzeesnor anyotherSIVotherthantherecombinantvirusthatgaverisetoSIVcpzhasbeenreportedin apes.Aschimpanzeesaretheclosestrelativesofhumans,themechanismsgoverningtheirsus- ceptibilityorresistancetolentiviruseshavedirectrelevanceforthepotentialofadditionalpri- matelentivirusestoadapttohominoidsandsubsequentlyspreadinhumans. Hostrestrictionfactorsareintrinsicblockstoviralreplication[12,13].Therefore,tocom- pletetheirlifecycle,virusesencodeantagoniststhattargettheseinnateimmunefactors.These antagonisticrelationshipshaveledtogeneticconflictsdrivingtheevolutionandspecificitiesof virus-hostinteractions,whichmayimposepotentspeciesbarrierstocross-speciestransmission [12].APOBEC3Gisoneoftheantiviralproteinsthathavebeenimplicatedinthespecies-speci- ficityoflentiviruses,althoughtheroleofAPOBEC3Gasaspeciesbarrierhasbeenmainly PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 2/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees investigatedinexperimentalcross-speciestransmissions[14–17].Moreover,thereareatleast fourgenesfromtheAPOBEC3genefamily(APOBEC3D,F,G,andH)thatpotentlyblockthe lentivirallifecycleintheabsenceofthespecificviralantagonistVif(reviewedin[18,19]).Vif primarilycounteractstheAPOBEC3sbybindingthehostproteinandtargetingitforproteaso- maldegradationbyrecruitinganE3ubiquitinligasecomplex.Althoughvifishighlydiverse withinandbetweenSIVandHIVlineages,itispresentinallprimatelentivirusesandhasan ancientandconservedroleinantagonizingthehostAPOBEC3Gprotein[20]. Here,weexaminedwhychimpanzeesharboronlyasingleSIVlineagedespitebeingfre- quentlyexposedtovariousSIVsthatinfecttheirpreyspecies.WeshowthatViffromdiverse lentivirusesisincapableofantagonizingchimpanzeeAPOBEC3G.Moreover,additionalchim- panzeeAPOBEC3familymembers,especiallyAPOBEC3D,alsoprovideblockstolentiviral replication.Consequently,wefindthatthepotentialofalentivirustoreplicateinprimary chimpanzeeCD4+TcellsisgovernedbyitsaccessoryproteinVif.Ourdatasuggestthatreten- tionandevolutionoftheAPOBEC3family,whereseveralhostproteinsareantagonizedbya singleviralproteinatdifferentmotifs,setupadiversebattlegroundagainstviruses,whichmay overallenhancetheprotectionofthehostagainstviralemergence.Finally,weshowthatthe APOBEC3genesarepolymorphicincommonchimpanzeesandbonobos,butthatthepopula- tionsaresimilarlyresistanttolentiviruseswithvariousvif.Overall,weproposethattherestric- tionimposedbytheAPOBEC3familyofhostrestrictionfactorsisacrucialmechanismby whichcommonchimpanzeesandbonobosmaybenaturallyprotectedagainstmostlentiviral cross-speciestransmissions. Results Viffrommostmonkeylentivirusesdonothavethecapacityto antagonizechimpanzeeAPOBEC3G Chimpanzeeshaveoverlappingrangeswithmanymonkeys[21]thatarewidelyandcommonly infectedbylentiviruses[1].EachSIVbearsalineage-specificvifwhosesequencevariesgreatly betweenlentivirallineages(Fig1A).ItwaspreviouslyshownthattheinclusionofSIVmacvif inHIV-1isnecessarytoexperimentallygenerateasimian-tropicHIV-1inrhesusmacaques [14,15].Moreover,inpopulationsofAfricangreenmonkeys(AGMs)naturallyinfectedby SIVs,vifco-evolvedwithAPOBEC3GpolymorphismsinthedifferentAGMspeciestomain- tainantagonism[17].Inaddition,wepreviouslyfoundthatadaptationofSIVcpztochimpan- zeesinvolvedtheevolutionofthevifgenetoadaptandcounteractchimpanzeeAPOBEC3G [4].Therefore,todeterminewhetherAPOBEC3Gcouldberesponsibleforthelackoftransmis- sionofdiverseSIVstochimpanzees,wetestedanextendedpanelofVifsfromtenlentivirallin- eagesthatspansthediversityofprimatelentivirusesforitsabilitytoantagonizechimpanzee APOBEC3G(Fig1A).ThispanelincludedvifgenesfromSIVsthatinfectknownpreysof chimpanzees(e.g.SIVwrcfromwestern-redcolobus[6,7]).EachSIVvifgenewasclonedinto anHIV-1backboneinplaceofHIV-1vifaspreviouslydescribed[20].ThecapacityofVifto antagonizechimpanzeeAPOBEC3Gwasmeasuredinsingle-roundinfectivityassaysbyco- transfectingtheHIV-1proviruscontaininganSIVvifgenewithaplasmidencodingchimpan- zeeAPOBEC3G[22].Thesupernatantwasnormalizedforp24gagexpressionandusedtoinfect aTcellline,SupT1.TheHIV-1provirusencodedadefectiveenvelopegeneandwaspseudo- typedwithVSV-Gsothatonlyoneroundofinfectionwasassayedandtheprovirusexpressed aluciferasegeneusedasthereadout. IntheabsenceofVif,chimpanzeeAPOBEC3Gwasabletoblocklentiviralinfection(Fig1B, whitebar).Aspositivecontrol,thiswasrescuedbySIVcpzVif,whichfullyantagonizedchim- panzeeAPOBEC3G(Fig1B,blackbars,SIVcpzPtsandSIVcpzPttVifs)[4].BytestingtheVif PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 3/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees Fig1.APOBEC3GprotectschimpanzeesfrommostSIVcross-speciesinfections.A,PhylogeneticanalysisofVifproteinsfromdifferentprimate lentivirusesasdescribedintheMethods.B,Single-roundinfectivityassayperformedinthepresenceorabsenceofchimpanzeeAPOBEC3G;infectivityin theabsenceofAPOBEC3Gwasnormalizedto100%.Thegraphsshowtheinfectivityvaluesfortheaverageofsixtonineinfections;errorbarsindicatethe SDfromthemeanofthesereplicates.TheinfectivityofHIV-1ΔVif(white,negativecontrol),andHIV-1ΔVifΔEnvLuc2plasmidwithviffromSIVcpzPtsTan3or SIVcpzPttGab1(black,positivecontrols),orviffromSIVsfromthegivenprimatespecies(greybars)weretested.EachoftheVifproteinswasfullycapableof antagonizingatleastoneAPOBEC3proteinusingidenticalproviralexpressionconstructstothoseinFig1B([4,17,20]andFig2). doi:10.1371/journal.ppat.1005149.g001 proteinfromeightdifferentSIVcpzisolates,wefoundthatallofthemwerealsoabletoantago- nizechimpanzeeAPOBEC3G(S1BFig).However,ViffromotherSIVlineageshaddifferential capacitiestoantagonizechimpanzeeAPOBEC3G(Fig1B,greybars).Aspreviouslyshown[4], ViffrombothSIVrcmandSIVmuswereabletopartiallyrestoreinfectivityinthepresenceof chimpanzeeAPOBEC3G(17–25%rescueofinfectivity),whichmayhavefacilitatedtheirevo- lutionandadaptationtochimpanzees.Amongsttheothermonkeylentiviralvifgenes,allbut onelackedthecapacitytorescueviralinfectioninthepresenceofchimpanzeeAPOBEC3G (lessthan4%infectivityrelativetoSIVcpzVif)(Fig1B).Inparticular,theViffromSIVwrcwas unabletocounteractchimpanzeeAPOBEC3Grestriction(Fig1B).Thisresultalonemay PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 4/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees Table1. AllvirusesthatnaturallyjumpedthespeciesbarrierhadsomecapacitytoantagonizethenewspeciesAPOBEC3G. SensitivityofAPO- BEC3G(fromtherecipienthostspecies)totheSIVVifprotein(fromthevirusthatcrossedthespeciesbarrier);infectivityofvirusesproducedinthepresence ofAPOBEC3Gisreportedasapercentage,relativetoinfectivityintheabsenceofAPOBEC3G(100%). SIVVifIsolatesa APOBEC3Gb Relativeinfectivityofvirusesc Originof...d Referencee SIVrcm Chimpanzee 17% SIVcpz Fig1B SIVmus Chimpanzee 25% SIVcpz Fig1B SIVcpz Human 73% HIV-1 Etienneetal.2013 SIVcpz Gorilla Minimal SIVgor Letkoetal.2013,D’Arcetal.2015 SIVgor Human ~85% HIV-1 Letkoetal.2013 SIVsmm Macaques 90% SIVmac Comptonetal.2013 SIVsmm Human 100% HIV-2 Comptonetal.2013 SIVver Baboon 86% SIVver-bab S2Fig SIVsab Patas 71% SIVsab-pat S2Fig a,Virusfromwhichthevifgenewastaken.Vifproteinsarefromvirusesthatcrossedtoanewhostspecies. b,HostspeciesfromwhichAPOBEC3Gwastaken.APOBEC3Gproteinsarefromrecipienthostspecies. c,InfectivityofviralconstructsproducedinthepresenceofAPOBEC3G(relativetonoAPOBEC3G). d,Virusthatresultedfromthecross-speciestransmissionevent(s). e,References:Etienneetal.2013[4],Comptonetal.2013[20],Letkoetal2013[56],D’Arcetal.2015[11],othersaredatafromthisstudy(Figs1Band S2). doi:10.1371/journal.ppat.1005149.t001 explainwhychimpanzeesarenotinfectedbySIVsfromoneoftheirmostcommonprey,the western-redcolobus. Ascontrols,wealsoexaminedtheVif-APOBEC3Gantagonismintwocasesofknown cross-speciestransmissions,thatofSIVagm.ver(orSIVver)intobaboons[23]andSIVagm.sab (orSIVsab)intoPatasmonkeys[24].Inbothcases,theViffromthedonorspecies(i.e.SIVver VifandSIVsabVif)wascapabletoovercometheAPOBEC3Goftherecipientspecies(i.e. baboonsandPatasmonkeys)aswellasitovercametheAPOBEC3Gofitsnaturalhost(S2 Fig).Atabulationofothercross-speciestransmissionsofprimatelentiviruses(Table1)indi- catesthatallknownnaturalhostswitchesthatoccurredwerefromprimatelentivirusesthat hadsomeorfullcapacitytoantagonizetheirnewhostAPOBEC3G(Table1andS2Fig).This suggeststhatatleastpartialantagonismofAPOBEC3Gmaybeapre-requisitetonatural cross-speciesinfection.Ontheotherhand,APOBEC3Gantagonismisnotsufficienttoallow cross-speciestransmission,asotherbarriersmaybeinvolved.Forexample,SIVsmmVifwas theonlymonkeylentiviralproteinabletocompletelyantagonizechimpanzeeAPOBEC3G (Fig1B),showingthatAPOBEC3Gcannotexplainthelackofinfectionofchimpanzeepopula- tionswiththisvirus(seebelow).Insummary,thelackofantagonismofAPOBEC3Gbylenti- viralVifscouldexplainthelackofSIVemergenceintochimpanzeesofmost,butnotallSIVs frommonkeys. TheVifproteinsfrommostmonkeySIVspoorlyantagonizetheantiviral activityofchimpanzeeAPOBEC3proteins BecauseotherAPOBEC3genesmayalsobeimplicatedintheVif-dependentrestrictionoflenti- viruses,wetestedifvifgenesfromthevariousSIVlineagesarecapableofantagonizingchim- panzeeAPOBEC3D,APOBEC3F,andAPOBEC3H.APOBEC3Disofparticularinterest, becausethechimpanzeeversionofthisproteinishighlyactiveagainstlentiviruses,whilethe humanversionhaslesssuchactivity[25].Usingthesingle-roundassaywhereexogenousAPO- BEC3genesaretransfectedinto293TcellsasdescribedinFig1B,weconfirmedthatinthe PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 5/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees absenceofVif,chimpanzeeAPOBEC3DismorepotentthanthehumanAPOBEC3Din restrictingalentivirus(S3AFig,delta-Vifcondition;similarexpressionlevelofchimpanzee andhumanAPOBEC3Dinadose-dependentmanner,S3BFig)[25].Despitetheincreased activityofchimpanzeeAPOBEC3Drelativetothehumanprotein,theVifproteinfromtwo divergentSIVcpzisolateswasabletoantagonizechimpanzeeAPOBEC3Dandtorescueviral infection(Fig2A,blackbars).Ontheotherhand,theVifproteinfromsixmonkeySIVline- ages,includingSIVwrcVif,wasnotabletoantagonizechimpanzeeAPOBEC3D(Fig2A). Moreover,itwasalsonotablethat,althoughitcouldreadilyantagonizechimpanzeeAPO- BEC3G,SIVsmmVifwasonlypoorlyactiveagainstchimpanzeeAPOBEC3D(Fig2A,15% capacityversusSIVcpzVif). ChimpanzeeAPOBEC3FandAPOBEC3Halsoreducedlentiviralinfectivityintheabsence ofVif,althoughAPOBEC3FrestrictionwasnotasstrongastheotherAPOBEC3s(Fig2Band 2C,whitebars).MostmonkeySIVlineagesencodeaVifthathadamoderateactivityagainst chimpanzeeAPOBEC3F(Fig2B),whilemostVifswerefullyequippedtoantagonizechimpan- zeeAPOBEC3H(Fig2C,levelsofinfectivitysimilartoSIVcpzVif).Thissuggeststhatchim- panzeeAPOBEC3HandAPOBEC3FontheirownmaynotbemajorspeciesbarrierstoSIVs ingeneral,althoughsomeSIVsweremoreefficientthanothersatantagonizingthechimpanzee APOBEC3Finparticular. Overall,onlytheVifproteinfromSIVcpzwasabletoantagonizealltestedmembersofthe chimpanzeeAPOBEC3family.TheantagonismofSIVcpzVifcorrespondstodecreasesinthe levelsofchimpanzeeAPOBEC3D,F,G,andH(S4Fig),consistentwiththeknownmecha- nismsofVif-mediateddegradationofAPOBEC3proteins[18].TheproteinViffromdifferent lentivirallineageshaddifferentspecificitiesforagivenAPOBEC3substrate(Fig2D,readthe heatmapvertically).Forexample,chimpanzeeAPOBEC3GcouldbeantagonizedbySIVsmm, butnotbySIVwrcorotherSIVs(Fig2D).Importantly,wealsofoundthatagivenvifhaddif- ferentspecificitiesamongsttheAPOBEC3genes(Fig2D,readtheheatmaphorizontally). Indeed,whilemostoftheVifproteinsretainedthecapacitytoantagonizechimpanzeeAPO- BEC3FandAPOBEC3H,onlyafewofthemwerecapabletocounteractchimpanzeeAPO- BEC3DandAPOBEC3G(Fig2D).Thissuggeststhattheevolutionandretentionofmultiple antiviralAPOBEC3proteinsinchimpanzeesprovideapotentrestrictiontoabroaddiversity oflentiviruses,andthereforelikelyconferanadvantagetothespeciesagainstcross-species infections.OurdataalsoshowthatthevariousSIVlineageshavedifferentsusceptibilityto chimpanzeerestrictionfactors.Forexample,SIVsmmstrainswouldbeexpectedtoadaptand antagonizechimpanzeeAPOBEC3proteinsmorereadilythanstrainsofSIVwrc,whichwould needtoadapttoantagonizethreeAPOBEC3members.Indeed,SIVwrcwasunabletocause degradationofchimpanzeeAPOBEC3G,F,andDproteins(S4Fig).Hence,inadditiontothe strongbarrierconferredbyAPOBEC3G,otherAPOBEC3members,especiallyAPOBEC3D, alsoposeanobstacletowardstransmissionandadaptationofdiverseSIVsharboredbymon- keystochimpanzees. Vif-dependentrestrictionofalentivirusinprimarychimpanzeeCD4+T cells WewishedtodetermineiftheVif-dependentrestrictionsobservedintheAPOBEC3over- expressionassays(Figs1and2)couldberecapitulatedininfectionsofprimarychimpanzee CD4+Tcells.WemodifiedtheprovirusesusedinFigs1and2byreplacingtheHIV-1env gene,sothattheHIV-1backbonecontainingdifferentSIVvifgeneswouldbereplication-com- petentwithanX4envelopefromHIV-1.Theadvantageofthissystem,asopposedtoinfection ofchimpanzeecellswithdifferententireSIVs,isthatwecouldcontrolfortheotherhostfactors PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 6/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 7/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees Fig2.ChimpanzeeAPOBEC3D,APOBEC3FandAPOBEC3HalsohaveantiviralcapacitiesthatmonkeySIVVifsdifferentiallyantagonize.Single- roundinfectivityassayperformedinthepresenceorabsenceofchimpanzeeAPOBEC3D(A),APOBEC3F(B),andAPOBEC3H(C),asdescribedinFig1B. D,HeatmapsummarizingtheantagonisticpotentialofViffromvariouslentiviruses(shownontheleft)againstchimpanzeeAPOBEC3genes(shownatthe top).TheintensityofthecolorcorrespondstothelevelthatagivenSIVVifcouldantagonizethecorrespondingchimpanzeeAPOBEC3protein(darkeris moreantagonism,lighterislessantagonism).ThecolorsweredeterminedaccordingtotheinfectivityvalueofthegivenviralVifconstructrelativetothe infectivityofthepositivecontrolbearingSIVcpzVif:lightestgreen,lessthan10%relativeinfectivity;intermediategreen,between10%and60%relative infectivity;darkgreen,morethan60%relativeinfectivity. doi:10.1371/journal.ppat.1005149.g002 thatmayinteractinaspecies-specificmannerwiththevirus,asonlythevifgenewasdifferent betweenthereplication-competentviruses.Moreover,certainHIV-1strainshavebeenshown toreplicateinprimarychimpanzeecells[26]. Becauseofthelimitingamountsofprimarychimpanzee(Pantroglodytesverus)CD4+T cells,weusedfourHIV-1clones,eachcontainingadifferentSIVVif;twoSIVVifsthatfully antagonizedchimpanzeeAPOBEC3Gintheover-expressionsystem(SIVcpzVif,whichserved asapositivecontrol,andSIVsmmVif),oneVifthatpartiallyantagonizedchimpanzeeAPO- BEC3G(SIVrcmVif),andonethatfailedtoantagonizechimpanzeeAPOBEC3G(SIVsabVif). AnHIV-1deletedinvifservedasanegativecontrol.Thisassaydiffersintwoimportantways fromthesingle-roundassayusedinFigs1and2.First,sincethevirusesarereplication-compe- tent,wemeasuredp24gagproductionratherthanareportergene.Second,andmoreimpor- tantly,viralinoculawereinitiallyproducedintransfected293Tcellsintheabsenceofany addedAPOBEC3gene.BecauseAPOBEC3Gisactiveinthetargetcell,ratherthanthepro- ducercell,thismeansthatthefirstroundofinfectionoftheprimarycellswillproceeduninhib- itedbyAPOBEC3GandtheeffectsofendogenouschimpanzeeAPOBEC3Gwouldbe observedonlyinthesecond(andsubsequent)roundsofinfection. Allviralconstructsreplicatedwithcomparablekineticsina“permissive”Tcellline,SupT1, whichdoesnotexpressendogenousAPOBEC3G(S5AFig)[27,28].Thisshowsthatnoneof theviralconstructshadaninherentreplicationdefect.InprimaryCD4+Tcellsfromthree chimpanzeedonors,wefoundthatthedelta-Vifconstructreplicatedaftertheinitialinfection (asexpectedsinceitwasproducedincellswithoutAPOBEC3G;Fig3A,greylines).However, itdidnotreplicatebeyondthefirsttime-pointmeasured(Fig3A,greylines).Ontheother hand,theconstructthatencodedanSIVcpzVifreplicatedbetweenonetotwoordersofmagni- tudebetterthanthatofthedelta-Vifconstruct(Fig3A,blackversusgreylines).Thesedata showthatthevifgeneisessentialforefficientviralreplicationinprimarychimpanzeeCD4+T cells. WefoundsimilarreplicationpatternsinallthreechimpanzeeCD4+Tcellculturesamong virusescontainingdifferentvifgenes(Fig3A).TheviralconstructcontainingSIVsabvifrepli- catedtosimilarlevelsasthenegativecontrol(absenceofvif),showingthatSIVsabVifwasnot activeinchimpanzeecells(Fig3A,orangeline).ThisresultisconsistentwiththedatathatSIV- sabVifisunabletoovercomechimpanzeeAPOBEC3G(Fig1B).Ascontrol,theinfectiouspro- viralconstructwithSIVsabVifwasfullycapableofovercomingAGMAPOBEC3Ginan infectionassay(S6Fig).Moreover,theseresultsindicatethatoftheAPOBEC3proteins,APO- BEC3GaloneiscapableofblockingvirusreplicationsinceSIVsabVifwasabletoantagonize chimpanzeeAPOBEC3D,F,orH(Fig2D). IncontrasttovirusesencodingSIVsabVif,virusesthatencodedSIVrcmVifandSIVsmm Vifhadintermediatecapacitiestoreplicateinthechimpanzeedonorcells(Fig3A,blueand greenlines).TheintermediatereplicationofthevirusencodingSIVrcmVif(Fig3A)isconsis- tentwiththeintermediateabilityofSIVrcmViftoovercomechimpanzeeAPOBEC3G(Fig 1B).However,theintermediatereplicationofthevirusencodingSIVsmmVif(Fig3A)isnot consistentwiththefullactivityofSIVsmmVifagainstchimpanzeeAPOBEC3G(Fig1B),but PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 8/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees Fig3.Vif-dependentrestrictionoflentiviralreplicationinprimarychimpanzeeCD4+Tcells.A,PrimaryCD4+Tcellsfromthreechimpanzeedonors wereinfectedwithreplication-competentHIV-1clonescontainingeithernoVif(ΔVif)orViffromdifferentSIVlineages(SIVcpz,SIVsab,SIVrcm,orSIVsmm) asdescribedinthemethods.ViralreplicationwasevaluatedbymeasuringHIVp24titersevery48hovera9-or10-daycourseofinfection.B,Thesame experimentwasperformed,butcellsweretreatedwith500U/mlofIFNα(left)and100U/mlofIFNβ(right)24hpriorinfection(dataareshownhereforcells fromdonor1;datafordonor2areshowninS5BFig). doi:10.1371/journal.ppat.1005149.g003 couldbeexplainedbythepooractivityofSIVsmmVifagainstchimpanzeeAPOBEC3D(Fig 2Aand2D).Therefore,whiletheVif-dependentrestrictionofSIVrcmandSIVsabinprimary chimpanzeeCD4+TcellscouldbeexplainedbyAPOBEC3G,theVif-dependentrestrictionof SIVsmmmustbeduetoanothercellularfactor,potentiallyAPOBEC3D. TheAPOBEC3proteinsarenotinducedbyinterferon(IFN)inactivatedhumanCD4+T cells[27].However,otherVif-dependentpotentialrestrictionfactormightbeinducedbyIFN. Thus,wealsoperformedtheseexperimentsinthepresenceofIFNtodetermineifwewould seedifferentpatternsofvirusgrowth.WefoundthattreatmentofprimarychimpanzeeCD4+ TcellswithIFNαorIFNβloweredtheoverallamountoflentiviralreplication,butdidnot changetherelativeVif-dependency(Figs3BandS5B).Thesedatasuggestthatthenon-IFN inducedAPOBEC3proteinsarethemajorViftargetsinactivatedprimarychimpanzeeCD4+ Tcells. PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 9/24 APOBEC3asaBarriertoSIVInfectionofChimpanzees TheAPOBEC3proteinsmediatetheirantiviraleffectsthroughthehypermutationofthe newlysynthesizedviralgenomebytheircytidinedeaminaseactivity,aswellasotherproposed mechanisms[19,29].AsoneofthehallmarksoftheAPOBEC3restrictionistheinductionof G-to-Ahypermutationinviruses(reviewedin[18]),welookedforevidenceofsuchhypermu- tationinintegratedviralgenomesninedaysafterinfectionofprimarychimpanzeeCD4+T cells.GenomicDNAwasextractedfrominfectedcellsandtwofragments(of~1,200bpandof ~600bp)encompassingthevifregionwereamplified,cloned,andsequenced(seeMethods). Twomethodswereusedtodeterminethesignificanceofhypermutationsignatures,Hypermut [30]andHyperfreq[31],whichbothdeterminethatasequenceishypermutatedwhenG-to-A mutationsinagivenhypermutation-associatedcontextaremorelikelythanmutationsina controlcontext.ThefirstmethodusestheFisherexacttest,whilethesecondoneusesaBayes- ianapproachandcanevaluatethestrengthofvarioushypermutationcontexts[31](see Methods). WefoundthattheviralconstructthatlackedavifgeneaccumulatedmanyG-to-Amuta- tionsinitsgenome(G-to-Amutationrateof0.65%,versus0.05%forothermutations;Table2, ΔVifcolumn)and50%ofthesequenceswerefoundtobesignificantlyhypermutatedinan APOBEC3-context(p<0.05)(Table2).ThesemutationsoccurredprimarilyintheGGcontext, whichischaracteristicofAPOBEC3Gactivity(85%ofthemutationswereintheGGcontext and,usingHyperfreq,hypermutationofsequenceswasmostfrequentlyassociatedwiththeGG context,Table2).However,G-to-AmutationsalsooccurredintheGAcontext,whichmaybe asignatureofAPOBEC3F,APOBEC3D,and/orAPOBEC3Hactivity(Table2)[25,32].Incon- trast,theviralconstructthatexpressedtheSIVcpzVifhadnoevidenceofhypermutation (Table2,cpzVifcolumn).ThissuggeststhattheexpressionoftheAPOBEC3proteinsinacti- vatedprimarychimpanzeeCD4+Tcellswasabletohypermutatetheviralgenomeinthe absenceofVifantagonism,withAPOBEC3Gbeingthemaindriver,andthatSIVcpzVifcould counteractthisAPOBEC3-mediatedhypermutation. Table2. G-to-AhypermutationsignaturesinviralgenomesafterninedaysofinfectioninchimpanzeeprimaryCD4+TcellsaredependentonVif. PrimaryCD4+Tcellsfromthechimpanzeedonor1wereinfectedwithreplicationcompetentvirusesHIV:ΔVif,sabVif,rcmVif,smmVif,orcpzVif.Cellswere harvestedafterninedaysofinfectionandgenomicDNAwasextracted.Viralfragmentsandcloneswereretrievedasdescribedinthemethods.Sequences wereanalyzedforG-to-A(“G>A”)hypermutationsignificanceusingHypermut[30]andHyperfreq[31],asdescribedinthemethods. ΔVif sabVif rcmVif smmVif cpzVif Sequencedclones 16 9 21 25 21 Totalbpsequenced 9169 7688 21446 27577 23891 G>AinGGcontexta 51 62 2 1 0 G>AinGAcontext 8 0 6 1 1 TotalnumberofG>A 60 62 10 2 1 G>Amutationrate(%) 0.65 0.81 0.05 0.01 0.00 IntactVifORFb NA 2/9 all all all Hypermut:Hypermutantclonesp<0.05c 6/16 6/9 0/21 0/25 0/21 Hyperfreq:Hypermutantclonesd(strongestpattern)e 8/16(7GG,1GR) 6/9(6GG) 2/21(2GA) 0/25 0/21 Othermutations 5 5 14 13 15 Othermutationrate(%) 0.05 0.07 0.07 0.05 0.06 a,numberofG-to-AmutationsintheGGcontext b,numberofintactVifopenreadingframe(ORF),NA,notapplicable c,Numberofclonesthataresignificantlyconsideredashypermutant(p<0.05)usingHypermut2.0[30] d,Numberofclonesthatthatwereconsideredaspositiveforhypermutationatthesignificancelevelof0.05[31] e,Strongestpattern,patterninwhichtheevidenceofhypermutationappearedtobethestrongest[31]. doi:10.1371/journal.ppat.1005149.t002 PLOSPathogens|DOI:10.1371/journal.ppat.1005149 September22,2015 10/24

Description:
mate lentiviruses to antagonize the APOBEC3 antiviral gene family found in .. The first method uses the Fisher exact test, while the second one uses a Bayes b, number of intact Vif open reading frame (ORF), NA, not applicable .. nucleotides analyzed per sample were 7,688–27,577 bp, as shown in
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