Washington University School of Medicine Digital Commons@Becker Open Access Publications 2015 Regulation of the transcription factor EB-PGC1α axis by beclin-1 controls mitochondrial quality and cardiomyocyte death under stress Xlucul Ma Washington University School of Medicine in St. Louis Halyan Liu Washington University School of Medicine in St. Louis John T. Murphy Washington University School of Medicine in St. Louis Sarah R. Foyil Washington University School of Medicine in St. Louis Rebecca J. Godar Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at:http://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Ma, Xlucul; Liu, Halyan; Murphy, John T.; Foyil, Sarah R.; Godar, Rebecca J.; Abulrqeba, Haedar; Weinheimer, Carla J.; Barger, Philip M.; and Diwan, Abhinav, ,"Regulation of the transcription factor EB-PGC1α axis by beclin-1 controls mitochondrial quality and cardiomyocyte death under stress." Molecualar and Cellular Biology.35,6. 956-976. (2015). http://digitalcommons.wustl.edu/open_access_pubs/3964 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please [email protected]. Authors Xlucul Ma, Halyan Liu, John T. Murphy, Sarah R. Foyil, Rebecca J. Godar, Haedar Abulrqeba, Carla J. Weinheimer, Philip M. Barger, and Abhinav Diwan This open access publication is available at Digital Commons@Becker:http://digitalcommons.wustl.edu/open_access_pubs/3964 (cid:2) Regulation of the Transcription Factor EB-PGC1 Axis by Beclin-1 Controls Mitochondrial Quality and Cardiomyocyte Death under Stress XiucuiMa,a,cHaiyanLiu,a,cJohnT.Murphy,aSarahR.Foyil,a,cRebeccaJ.Godar,a,cHaedarAbuirqeba,aCarlaJ.Weinheimer,a PhilipM.Barger,aAbhinavDiwana,b,c DivisionofCardiologyandCenterforCardiovascularResearch,DepartmentofInternalMedicine,WashingtonUniversitySchoolofMedicine,St.Louis,Missouri,USAa; DepartmentofCellBiologyandPhysiology,WashingtonUniversitySchoolofMedicine,St.Louis,Missouri,USAb;JohnCochranVAMedicalCenter,St.Louis,Missouri, USAc Incardiacischemia-reperfusioninjury,reactiveoxygenspecies(ROS)generationandupregulationofthehypoxia-induc- ibleproteinBNIP3resultinmitochondrialpermeabilization,butimpairmentinautophagicremovalofdamagedmito- chondriaprovokesprogrammedcardiomyocytedeath.BNIP3expressionandROSgenerationresultinupregulationof beclin-1,aproteinassociatedwithtranscriptionalsuppressionofautophagy-lysosomeproteinsandreducedactivationof transcriptionfactorEB(TFEB),amasterregulatoroftheautophagy-lysosomemachinery.Partialbeclin-1knockdown transcriptionallystimulateslysosomebiogenesisandautophagyviamTORinhibitionandactivationofTFEB,enhancing removalofdepolarizedmitochondria.TFEBactivationconcomitantlystimulatesmitochondrialbiogenesisviaPGC1(cid:2)in- ductiontorestorenormallypolarizedmitochondriaandattenuateBNIP3-andhypoxia-reoxygenation-inducedcelldeath. Conversely,overexpressionofbeclin-1activatesmTORtoinhibitTFEB,resultingindeclinesinlysosomenumbersand suppressionofPGC1(cid:2)transcription.Importantly,knockdownofendogenousTFEBorPGC1(cid:2)resultsinacompleteor partialloss,respectively,ofthecytoprotectiveeffectsofpartialbeclin-1knockdown,indicatingacriticalroleforbothmi- tochondrialautophagyandbiogenesisinensuringcellularviability.Thesestudiesuncoveratranscriptionalfeedbackloop forbeclin-1-mediatedregulationofTFEBactivationandimplicateacentralroleforTFEBincoordinatingmitochondrial autophagywithbiogenesistorestorenormallypolarizedmitochondriaandpreventischemia-reperfusion-inducedcardio- myocytedeath. Preservation of healthy mitochondria is essential for energy todrivereformationofnewlysosomes(18–20).Thisisfacili- generationandmaintenanceofcontractilefunctionincar- tated via a transcriptional induction of autophagy-lysosome diacmyocytes(1).Incardiacischemia-reperfusion(IR)injury, machinery proteins orchestrated by nuclear translocation of mitochondrial permeabilization results in activation of pro- the basic helix-loop-helix (bHLH) transcription factor EB grammed cell death pathways and cardiomyocyte loss (2). (TFEB)(21–25),amasterinduceroftheautophagy-lysosome Removal of damaged mitochondria by macroautophagy, a machinery (23), thereby sustaining autophagic flux. In con- lysosomaldegradativepathway,isessentialtopreventcardiomy- trast,lysosomenumbersprogressivelydeclinewithBNIP3-in- ocytedeathandlimitmyocardialinfarctsize(3,4).Cardiomyo- ducedautophagy,withoutreplenishment(15),suggestingthat cyteautophagyisupregulatedwithIRinjury(5),butautophago- animpairmentinthistranscriptionalresponseengenders“in- some processing is impaired early after reperfusion, which sufficient”cytoprotectiveautophagy. preventsautophagicremovalofdamagedmitochondria(6).The Relevant to this discussion is our observation that upon hypoxicinsultalsoprovokestranscriptionalinductionofBNIP3 reperfusion/reoxygenation, a rapid reactive oxygen species (Bcl2andnineteen-kilodaltoninteractingprotein3),aprodeath (ROS)-induced increase in beclin-1 abundance paradoxically Bcl2familyprotein(7,8)whichistargetedtoandpermeabilizes impairs autophagic flux in cardiomyocytes (6). Interestingly, mitochondria(9–11)andtriggerscardiomyocytedeathinIRin- whilebasalbeclin-1levelsplaycriticalrolesinautophagosome jury(12).WhileBNIP3hasbeensuggestedtofacilitatemitochon- drialautophagybyfunctioningasanadaptortosequesterdam- aged mitochondria within autophagosomes (13, 14), increased BNIP3expressionprovokesdeclinesinlysosomenumbers,with Received25August2014 Returnedformodification15September2014 Accepted30December2014 impairedautophagicflux,resultinginaccumulationofdamaged Acceptedmanuscriptpostedonline5January2015 mitochondriaandcardiomyocytedeath(15).Theseobservations CitationMaX,LiuH,MurphyJT,FoyilSR,GodarRJ,AbuirqebaH,WeinheimerCJ, implicateafailureoftheautophagy-lysosomemachinerytoclear BargerPM,DiwanA.2015.RegulationofthetranscriptionfactorEB-PGC1(cid:2)axisby damagedmitochondriaasacauseofcelldeathwithIRinjury,but beclin-1controlsmitochondrialqualityandcardiomyocytedeathunderstress. theunderlyingmechanismsremaintobedefined. MolCellBiol35:956–976.doi:10.1128/MCB.01091-14. Mitochondria are also targeted for degradation by starva- AddresscorrespondencetoAbhinavDiwan,[email protected]. tion, wherein autophagy is critical for cell survival (16, 17). Copyright©2015,AmericanSocietyforMicrobiology.AllRightsReserved. Interestingly,withstarvation,lysosomenumbersrapidlyplum- doi:10.1128/MCB.01091-14 met(18),butendogenousmechanismsarepromptlyrecruited 956 mcb.asm.org MolecularandCellularBiology March2015 Volume35 Number6 Beclin-1RegulatesMitochondrialQualityviaTFEB formation(26)andprotectionagainstcardiomyocytedeath(6),we Generationofadenoviralconstructs.Lentiviralparticlescodingfor observedthatincreasedbeclin-1abundanceissufficienttosuppress mCherry-GFP-LC3 expression have been described (6). Adenoviral transcriptionofautophagy-lysosomemachinerygenes(6).Taken delivery of constructs was employed to achieve a high efficiency of together with the in vivo observation that haploinsufficiency of transductionandpermitevaluationofdose-dependenteffectsinpri- beclin-1bytargeteddisruptionofaBECN1alleleconferscytopro- maryNRCMs,aspreviouslydescribed(6,15).Adenoviralparticlesfor expression of short hairpin RNAs (shRNAs) targeting rat TFEB, tectionincardiacIRinjury(5),thesedatasuggestthehypothesis BECN1,andPPARGC1(cid:2)weregeneratedwiththeBLOCKiTadenoviral thatROS-inducedupregulationofbeclin-1transcriptionallyim- system (Invitrogen). Specific oligonucleotide sequences employed pairs the lysosomal machinery to prevent removal of damaged were as follows (with targeted coding sequences underlined): (i) mitochondria and cause cell death with BNIP3 expression and shRNAtargetingratTFEB,5=-CACCGAATCAAGGAGCTGGGAATG hypoxia-reoxygenationinjury.Inthisstudy,weuncoveredanau- CTGATCGAAATCAGCATTCCCAGCTCCTTGATTC-3=(top-strand toregulatoryloopwherebybeclin-1levelsregulateTFEBactivity, oligonucleotide) and 5=-AAAAGAATCAAGGAGCTGGGAATGC which coordinates mitochondrial autophagy with biogenesis to TGATTTCGATCAGCATTCCCAGCTCCTTGATTC-3= (bottom-strand controlmitochondrialqualityandregulatestress-inducedcardi- oligonucleotide);(ii)shRNAtargetingBECN1(annotatedshBECN1-2), omyocytedeath. 5=-CACCGCTCAGTACCAGCGAGAATATCGAAATATTCTCGCTGG TACTGAGC-3= (top-strand oligonucleotide) and 5=-AAAAGCT CAGTACCAGCGAGAATATTTCGATATTCTCGCTGGTACTGA MATERIALSANDMETHODS GC-3= (bottom-strand oligonucleotide); and (iii) shRNA targeting rat Invivoischemia-reperfusionmodeling.BECN1heterozygousnullmice PPARGC1(cid:2), 5=-CACCGAGCAAGTATGACTCTCTGCGAACAGAGAG (BECN1(cid:3)/(cid:4);micewithhaploinsufficiencyofbeclin-1)(26)andwild- TCATACTTGCTC-3= (top-strand oligonucleotide) and 5=- type (WT) mice of the C57BL/6 strain were obtained from Jackson AAAAGAGCAAGTATGACTCTCTGTTCGCAGAGAGTCAT Laboratories and subjected to reversible left anterior descending ACTTGCTC-3=(bottom-strandoligonucleotide). (LAD)coronaryarteryocclusiontoinduceischemiafor30min,fol- Adenoviral particles for shRNAs targeting BECN1 (annotated lowedby4hofreperfusion,asdescribedpreviously(6).Briefly,mice shBECN1-1) (5) and LacZ, as a nontargeting control for studies with were anesthetized with a mixture of ketamine (80 mg/kg of body shRNA-mediatedknockdown,andforoverexpressionofLacZ(asacon- weight) and xylazine (5 mg/kg), surgically prepped, and ventilated. trol), green fluorescent protein (GFP)-tagged LC3, FLAG-hBNIP3, Afterthoracotomy,theLADarterywasidentified,anda9-0polypro- mBECLIN-1, and hemagglutinin (HA)-tagged hTFEB have been de- pylenesuturewaspassedundertheLADartery.Aknotwastiedovera scribed previously (15). Adenoviral particles for expression of FLAG- 1-mmsectionofPE-10tubingplaceddirectlyoverthevesseltocreate PPARGC1(cid:2)wereengineeredwithataggingcodingsequenceforhuman theocclusion.Ischemiawasconfirmedbyanabsenceofbloodflow, PPARGC1(cid:2)withaFLAGtagattheNterminus,usingGatewaycloning verifiedvisually,andbythepresenceofSTelevationsonelectrocar- technology(Invitrogen).Viralparticlesweregeneratedperthemanufac- diogram (EKG). Reperfusion was induced to release the occlusion, turer’sinstructions.Inallexperiments,controladenoviralparticleswere whichwasconfirmedbyresolutionofSTsegmentelevation.Atsacri- added to groups as necessary to ensure equal viral particle doses, i.e., fice,theventriclesweresectionedintothreepieces;theapical1/3was multiplicitiesofinfection(MOIs),betweengroups. subjectedtobiochemicalanalysisasthe“injured”region,andthebasal Assessmentofcelldeath.Celldeathassayswereperformedin96-well 1/3wasprocessedasthe“remote”region.Sham-treatedmiceunder- plates(Nunc,Fisher)withaLive-Deadcytotoxicityviabilitykitformam- wenttheentiresurgicalprocedurewithoutocclusionoftheLADar- malian cells (Invitrogen), using a Tecan Infinite M200 Pro microplate tery. Autophagic flux was assessed in comparison to that of mice reader(Tecan)followingthemanufacturer’sinstructions,asdescribed pretreatedwithchloroquine(CQ;40mg/kg,administeredintraperi- previously(6). toneally[i.p.])30minpriortoIRmodeling,aspreviouslydescribed(6, AssessmentofTUNELpositivity.Terminaldeoxynucleotidyltrans- 27).AllanimalstudieswereapprovedbytheAnimalStudiesCommit- ferase-mediateddUTP-biotinnickendlabeling(TUNEL)wasperformed teeattheWashingtonUniversitySchoolofMedicineandtheInstitu- onfixedandpermeabilizedNRCMsbyusingtheDead-Endfluorometric tionalAnimalCareandUseCommitteeattheJohnCochranVAMed- TUNEL system (Promega) following the manufacturer’s directions, as icalCenter. Cellculture.Isolationofneonatalratcardiacmyocytes(NRCMs) previouslydescribed(15). wasperformedasdescribedpreviously(6).Heartswereremovedfrom CellularATPcontentanalysis.NRCMsweretransducedwithadeno- 1-day-old Sprague-Dawley rats, the atria and great vessels were viralparticlesfor24handthentrypsinized,and5(cid:7)104cellswereplated trimmedoff,andtissuewasfinelyminced,followedbysequentialdi- ineachwellofa96-wellplate.CellularATPlevelswerequantifiedusinga gestionwith0.5mg/mlcollagenase(WorthingtonBiochemical,NJ). luciferasereaction-basedassaykit(CellTiter-Gloreagent;Promega),and Ventricularcardiomyocyteswereseparatedfromfibroblastsbydiffer- readingswerenormalizedtothoseofviablecellsassessedbythetrypan entialplatinginmediumcontainingDulbecco’smodifiedEagle’sme- blueexclusionmethodaspreviouslydescribed(28). dium(DMEM),10%horseserum,5%fetalcalfserum,100(cid:5)mol/liter Immunofluorescenceimaging.ImagingformCherry-GFP-LC3and bromodeoxyuridine, penicillin, streptomycin, and L-glutamine, fol- LysoTrackerRedwasperformedwithliveNRCMs,andimagingforGFP- lowedbytissuecultureingelatin-coatedplatesinmediumcontaining LC3,LAMP1,andTFEB(withimmunofluorescenceoftheHAtag)was modifiedDMEM,100(cid:5)Mbromodeoxyuridine,penicillin,streptomy- performedwithNRCMsfixedwith4%paraformaldehyde(20min)and cin, L-glutamine, 10 ng/ml insulin, 10 (cid:5)g/ml transferrin, and 0.5 thenpermeabilizedwith0.1%TritonX-100(5min),usinganAxioscap mg/mlbovineserumalbumin. uprightmicroscopefittedwithanAxioCamHRCcameraandPlanNeo- Nutrient deprivation was induced by culture in serum-free Hanks fluarobjectives(20(cid:7)[numericalaperture{NA}(cid:8)0.60],40(cid:7)[NA(cid:8) balancedsaltsolution(HBSS;Invitrogen).HEK293cellswereculturedas 0.75],and63(cid:7)[oil][NA(cid:8)1.25][Zeiss]),alongwithappropriatefilter describedpreviously(15). cubes,aspreviouslydescribed(6).NuclearlocalizationofTFEBwasas- Hypoxia modeling. Cells were subjected to hypoxia in vitro in an sessedin60cells/group.LAMP1-positivepunctain50cells/groupwere oxygen control cabinet (Coy Laboratories, Grass Lake, MI) mounted countedusingImageJsoftwareasdescribedpreviously(15),andresults withinanincubatorandequippedwithanoxygensensorforcontinuous are expressed as numbers of dots/nucleus. Imaging for BNIP3 and oxygenlevelmonitoring.Amixtureof95%nitrogenand5%CO was COX-IVwasperformedonfixedandpermeabilizedNRCMswithaZeiss 2 infusedtocreatehypoxia,andoxygenlevelsinthechamberweremoni- confocalLSM700laserscanningconfocalmicroscopeusing63(cid:7)Zeiss toredandmaintainedat(cid:6)1%,asdescribedpreviously(6). Plan-Neofluar 40(cid:7)/1.3 and 63(cid:7)/1.4 oil immersion objectives. Nuclei March2015 Volume35 Number6 MolecularandCellularBiology mcb.asm.org 957 Maetal. werestainedbluewithHoechstdye(forlive-cellimaging)(H3750;In- HEK293cellsweretransfectedwiththePGL3.Lucvector,drivenbythe vitrogen) or DAPI (4=,6-diamidino-2-phenylindole) (for fixed cells) humanPPARGC1(cid:2)promoterwithout(i.e.,wild-typepromoter)orwith (H1200;VectorLaboratories).Epifluorescenceandconfocalimageswere mutationsinthe“CLEARsequence,”located69bpupstreamofthetran- acquired and analyzed using Zeiss Axiovision and Zen 2010 software, scriptionalstartsite(i.e.,(cid:4)18CLEARsitemutant),togetherwithpRL- respectively. SV40forRenillaluciferaseexpression(ataratioof100:1).Inaddition, Flow cytometric assessment. NRCMs were incubated with Lyso- cellswerecotransfectedwithexpressionvectorscodingfortheconstitu- TrackerRed(1mmol/literfor15min)toassesslysosomeabundance,with tivelyactivetranscriptionfactorCREB,theCREBactivatorTORC2(i.e., nonyl-acridineorange(NAO)(acardiolipin-bindingdye;10nmol/liter CRTC2)(seebelowfordetails),TFEB(pAd-CMV/V5-hTFEB),orLacZ for15min)andMitotrackerGreen(200nmol/literfor45min)toassess (pAd-CMV/V5-LacZ)(asacontrol),andluciferaseactivitiesweremea- mitochondrialmass,withJC-1(10mg/mlfor10min)ortetramethylrho- sured48haftertransfection.Fireflyluciferasereadingswerenormalized damine,ethylester(TMRE;50nmol/literfor30min)toassessmitochon- tothoseforRenillaluciferasetocontrolfortransfectionefficiency. drialpolarization,andwithcarboxy-H DCFDA(acell-permeatingROS Subcellular fractionation. NRCMs were subjected to biochemical 2 indicator;10(cid:5)mol/literfor30min)toassessthelevelsofROS.Following fractionationtorecovernucleus-enrichedandcytoplasmicfractions, incubation with these compounds at 37°C in 5% CO , the cells were aspreviouslydescribed(23).Heartswerefractionatedintonucleus- 2 trypsinizedandsubjectedtoflowcytometryonaFACScaninstrument enrichedandcytoplasmicsamplesbyusingaCelLyticNuCLEARex- (Becton-Dickinson)aspreviouslydescribed(15).Cyflogicsoftware(Cy- tractionkit(Nxtract;Sigma).Expressionofproteinslocalizedtothe Flo)wasemployedtoanalyze20,000eventsperrun. nucleus(histoneH3)andcytoplasm(glyceraldehyde-3-phosphatede- Assessment of mitochondrial DNA content. Mitochondrial DNA hydrogenase [GAPDH]) was examined to confirm relative enrich- contentwasassessedbyquantitativePCRanalysisaspreviouslydescribed ment. (29).Briefly,DNAwaspreparedfromNRCMpellets,andreal-timequan- Coimmunoprecipitation studies. Murine embryonic fibroblasts titativePCRwasperformedforthemitochondrialgeneNADH2(with (MEFs)fromC57BL/6wild-typemicewereadenovirallytransducedwith primers5=-ATCACCACCATTCTCGCAAT-3=and5=-TCCTATGTGGG beclin-1–HA(MOI(cid:8)100)ortransfectedwithN-terminalHA-tagged CAATTGATG-3=)andthenucleargeneRCAN1(withprimers5=-GGTT TSC1(Addgene)(32).Threehundredmicrogramsofproteinwasincu- TGCTGAGCCTCGAAG-3=and5=-CTTCATCCCTCCTTTGTAAC-3=). batedwithanti-HA(H3663;Sigma)ornormalrabbitIgG,andimmuno- Theratioofcopiesofmitochondrialtonucleargenesrepresentstherela- precipitationwasperformedusingDynaBeads(Invitrogen). tivemitochondrialDNAcontent. Immunoblotting. Immunoblotting was performed on cellular ex- Assessmentofmitochondrialfragmentation.Mitochondrialmor- tracts by use of previously described techniques (15). Antibodies em- phologywasascertainedtobefragmentedortubularbyvisualinspection ployedwereasfollows:antibodiesforFLAG(F3165;Sigma),HA(H6908; ofindividualcellsatahighmagnification,asdescribedpreviously(30). Sigma),LAMP1(AB24170;Abcam),beclin-1(ab16998[Abcam]andsc- Fifty cells were evaluated per experimental group, and results are ex- 11427[SantaCruz]),p70S6K(2708;CellSignaling),p-p70S6K(9234;Cell pressedaspercentagesofcellsshowingpredominantlyfragmentedmito- Signaling),4-EBP1(9644;CellSignaling),p-4EBP1(2855;CellSignaling), chondria. p-mTOR(2974;CellSignaling),mTOR(2983;CellSignaling),histoneH3 Assessmentofmitochondrialpolarization.Mitochondrialdepolar- (9715;CellSignaling),TFEB(MBS120432;employedtodetectadenovi- izationwasassessedbyexpressionofTMREorwiththeratiometricdye rallytransducedHA-taggedhumanTFEBwhenHAdetectionwaspre- JC-1,whichaggregatesintoredfluorescentpolymersinnormallypolar- cludedforspecificity),GAPDH(ab22555;Abcam),peroxisomeprolifera- izedmitochondriabutispredominantlyobservedasgreenfluorescent tor-activated receptor gamma coactivator 1(cid:2) (PGC1(cid:2)) (ab106814; monomers in cells with depolarized mitochondria, as previously de- Abcam),tuberoussclerosiscomplex1(TSC1)(6935;CellSignaling),and scribed(6,15). tuberoussclerosiscomplex2(TSC2)(3612;CellSignaling).MurineTFEB TEM.NRCMswerefixedinmodifiedKarnovsky’sfixative(3%glu- was detected with a Bethyl Labs antibody (A303-673A). The multiple taraldehyde,1%paraformaldehydein0.1Msodiumcacodylatebuffer), immunoreactiveTFEBbandsobserved(seeFig.12CandD)likelyrepre- followedbypostfixationin2%osmiumtetroxidein0.1Msodiumcaco- sent various TFEB isoforms (NP_001155194.1 and NP_035679.3) or dylatebufferfor1h.Thecellswerethenstainedwith2%aqueousuranyl posttranslationally modified forms of the protein in the myocardium. acetatefor30min,dehydratedinaseriesofgradedethanolconcentra- Immunoblotting for (cid:2)-sarcomeric actin ((cid:2)SA) (ab52219; Abcam) was tions,andembeddedinPolyBed(Polysciences).Blocksweresectionedat employedasaloadingcontrolunlessotherwiseindicated.ImageJsoftware a90-nmthickness,poststainedwithVenable’sleadcitrate,andviewed wasemployedforquantitativeanalysis.Proteinabundancewasnormal- with a JEOL model 1200EX transmission electron microscope (TEM) izedto(cid:2)-sarcomericactinproteinexpressionandreportedasthefold (JEOL,Tokyo,Japan).DigitalimageswereacquiredusinganAMTAd- changeversusthecontrol.Chemicalsemployedwereasfollows:3-methyl- vantageHR(AdvancedMicroscopyTechniques,Danvers,MA)high-def- adenine(3MA;EMD4Biosciences),torin-1(Tocris),MG-132(Cayman initioncharge-coupleddevice(CCD)1.3-megapixelTEMcamera. ChemicalCompany),andMnTMPyP(Calbiochem).Equivalentquanti- Assessmentofpromoter-drivenluciferaseactivity.Atotalof3(cid:7)104 ties of appropriate diluent were employed as controls in all studies in cells were plated per well of a 96-well plate and transfected with the whichthesechemicalswereemployed. PGL3.Lucvector,carryinga2,760-bpfragmentofthehumanPPARGC1(cid:2) QuantitativePCRanalysisformRNA.Real-timePCRwasperformed promoter(forfireflyluciferaseexpression),andthepRL-SV40vector(for asdescribedpreviously(6).Briefly,totalRNAwaspreparedfromNRCMs Renillaluciferaseexpression[31])ata100:1ratio,usingLipofectamine byuseofanRNA-easyminikit(Qiagen),andcDNAwassynthesizedwith 2000 (Invitrogen). Constructs coding for the human PPARGC1(cid:2) pro- 1(cid:5)goftotalRNAbyusingtheSuperScriptIIIfirst-strandsynthesissystem moter(GenBankaccessionnumberNG_028250.1)withindividualmu- (Invitrogen).OnemicroliterofcDNAtemplatewasmixedwith12.5(cid:5)lof tationsinthethreeCLEARsitesdetectedwithin(asdepictedinFig.9D) 2(cid:7)SYBRgreenPCRmastermix(Invitrogen)andsubjectedtoquantita- weregeneratedbysite-directedmutagenesisusingaQuikChangeLight- tivePCRintriplicateunderthefollowingconditions:50°Cfor2minand ningsite-directedmutagenesiskit(Stratagene)andverifiedbysequenc- 95°Cfor10minfollowedby40cyclesof95°Cfor15sand60°Cfor1min ing.Luciferaseactivitywasmeasuredwithadual-luciferaseassaykit(Pro- inanABI7500Fastreal-timePCRsystem.TheGAPDHgenewasalso mega) and a Tecan Infinite M200 Pro microplate reader (Tecan) amplifiedinparallelasareferenceforthequantificationoftranscripts. followingthemanufacturers’instructions.Fireflyluciferasevalueswere PrimersetsemployedareshowninTable1.Resultswerecalculatedusing normalizedtothoseforRenillaluciferasetocontrolfortransfectioneffi- the(cid:9)(cid:9)C methodandexpressedaspreviouslydescribed(6). T ciency.Toassesswhetherthebp(cid:4)18sitemutantconstructretainedac- ChIP assays. Chromatin immunoprecipitation (ChIP) was per- tivitytodrivetranscriptionalactivation(otherthanthatdrivenbyTFEB), formedaspreviouslyreported(25,33).Briefly,HEK293Acellsweretrans- 958 mcb.asm.org MolecularandCellularBiology March2015 Volume35 Number6 Beclin-1RegulatesMitochondrialQualityviaTFEB TABLE1PrimersequencesemployedforqPCRanalysisoftheindicatedgenes Primersequence(5=–3=) Targetgene Forward Reverse Ratgenes MAP1LC3B TTTGTAAGGGCGGTTCTGAC CAGGTAGCAGGAAGCAGAGG SQSTM1 GCTGCCCTGTACCCACATCT CGCCTTCATCCGAGAAAC LAMP1 TCTTCAGCGTGCAAGTCCAG ATGAGGACGATGAGGACCAG PPARGC1(cid:2) ATGAATGCAGCGGTCTTAGC AACAATGGCAGGGTTTGTTC BECN1 TTCAAGATCCTGGACCGAGTGAC AGACACCATCCTGGCGAGTTTC TFEB GTCCAGCAGCCACCTGAACGT ACCAGGGAAGCCGTGACCTG LAMP2A CCAAATTGGGATCCTAACCTAA TGGTGAAGCAGTGTTTATTAATTCC LAMP2B GGTGCTGGTCTTTCAGGCTTGATT ACCACCCAATCTAAGAGCAGGACT CTSB AAATCAGGCGTATACAAGCATGAA AGCCCAGAATGCGGATGG CTSD CTGAGTGGCTTCATGGGGAT CCTGACAGTGAAGAAGGAGC RAB7 TTACTTCGAGACCAGTGCCAAGGA TGTCCAGTTTGATGGGTTCAGGGA GAPDH GGCCGAGGGCCCACTA TGTTGAAGTCACAGGAGACAACCT RPS12 AAGGCATAGCTGCTGGAGGTGTAA AGTTGGATGCGAGCACACACAGAT RPL32 CCTCTGGTGAAGCCCAAGATC TCTGGGTTTCCGCCAGTTT Mousegenes MAP1LC3B CGTCCTGGACAAGACCAAGT ATTGCTGTCCCGAATGTCTC LAMP1 TCTTCAGTGTGCAGGTCCAG ATGAGGACGATGAGGACCAG PPARGC1(cid:2) ATGAATGCAGCGGTCTTAGC AACAATGGCAGGGTTTGTTC BECN1 AATCTAAGGAGTTGCCGTTATAC CCAGTGTCTTCAATCTTGCC TFEB GTCTAGCAGCCACCTGAACGT ACCATGGAGGCTGTGACCTG LAMP2A CCAAATTGGGATCCTAACCTAA TGGTCAAGCAGTGTTTATTAATTCC LAMP2B GGTGCTGGTCTTTCAGGCTTGATT ACCACCCAATCTAAGAGCAGGACT RAB7 TTACTTCGAGACCAGTGCCAAGGA TGTCCAGTTTGATGGGTTCAGGGA CTSB AAATCAGGAGTATACAAGCATGA GCCCAGGGATGCGGATGG CTSD CTGAGTGGCTTCATGGGAAT CCTGACAGTGGAGAAGGAGC SQSTM1 GCTGCCCTATACCCACATCT CGCCTTCATCCGAGAAAC GAPDH ACTCCCACTCTTCCACCTTC TCTTGCTCAGTGTCCTTGC RPS12 AAGACCGCCCTCATCCACGATG TTGGTGCTCAGCACAAAGTGCC RPL32 CCTCTGGTGAAGCCCAAGATC TCTGGGTTTCCGCCAGTTT fectedwiththeemptypAAV-CMV-TFEB-IRES-GFPconstruct,described verified, following which statistical differences were assessed with un- earlier(34),orwithemptyvector(asacontrol)for48h.Cellswerecol- paired2-tailedStudent’sttestfortwoexperimentalgroups,one-wayanal- lected,fixedwith1%formaldehydefor10min,andlysedonicewithChIP ysisofvariance(ANOVA)formultiplegroups,andtwo-wayANOVAfor lysisbuffer(50mMTris-HCl,pH7.5,100mMNaCl,1%TritonX-100, testingoftwovariablesacrossmultiplegroups,usingSPSSsoftware.Bon- 1%Tween20)for20min.Thelysatewasdigestedwithmicrococcalnu- ferroni’sandDunnett’sT3posthoctestswereemployedafterANOVAfor clease(Sigma)for15minat37°C,andthereactionwasterminatedusing testingforsignificantdifferencesbetweengroupsfordatawithequaland EDTA(2mM)andsodiumdodecylsulfate(SDS;1%).SDS-Out(Pierce) unequalvariances,respectively.Nonparametrictestswereemployedfor wasemployedtoprecipitatetheunboundSDS,andlysatesdiluted1:1 datathatwerenotnormallydistributed.Atwo-tailedPvalueof(cid:6)0.05was withChIPdilutionbuffer(50mMTris-HCl,pH7.5,100mMNaCl,0.5% consideredstatisticallysignificant. TritonX-100,2mMEDTA)wereincubatedwithhigh-capacityNeutr- Avidinagarose(Pierce).Biotinylatedanti-FLAGantibody(F9291;Sigma) RESULTS or isotype control IgG1 (M9035; Sigma) was precoupled with Neutr- BNIP3expressionincreasesbeclin-1abundancewithtranscrip- Avidinbeadsfor30minat4°C,andtheprotein-DNAcomplexeswere tionalsuppressionofautophagy-lysosomemachinery.BNIP3,a immunoprecipitated overnight at 4°C. After six washes, the DNA was elutedbyadditionof8mMbiotin,1%SDSinTris-EDTA(TE)bufferand Bcl-2familyprodeathprotein,istranscriptionallyinducedincar- precipitatedafterreversingthecross-linkagebyuseof200mMNaClat diacIRinjuryandprovokesmitochondrialpermeabilization(8, 65°Covernight.PCRwasperformedusingprimersflankingtheCLEAR 11,12).WehaveobservedthatBNIP3expressionprovokespro- site18bpupstreamofthetranscriptionalstartsite(forwardprimer,5=-C gressivedeclinesinlysosomenumbers,withaccumulationoffrag- GTCACGAGTTAGAGCAGCA-3=;andreverseprimer,5=-TCGCCCTTA mentedanddepolarizedmitochondria,leadingtocelldeath(15), AGCTTTTTCAA-3=)(204-bpamplicon).Anadditionalprimersetwithin and that restoring lysosome biogenesis by exogenous TFEB ex- an adjacent segment located between the CLEAR sites at bp (cid:4)18 and pressionreestablishesmitochondrialautophagytorescueBNIP3- (cid:4)469 (forward primer, 5=-CTGTCATGAAACAGGGAGCTTT-3=; and inducedcelldeath(15).Toexaminethemechanismsforimpaired reverseprimer,5=-GCTTTGAATGCCACAGACTCTA-3=)(125-bpam- autophagicremovalofBNIP3-damagedmitochondria,weevalu- plicon)didnotgenerateaproduct,demonstratingspecificity(datanot atedtheregulationoftheautophagy-lysosomemachinerybyad- shown). Statisticalanalysis.Resultsareexpressedasmeans(cid:10)standarderrors enoviraltransductionofNRCMswithBNIP3.Wehypothesized ofthemeans(SEM),withthesamplesize(n)pergroupindicatedinthe thatthedeclineinlysosomenumberisdrivenbyBNIP3-induced figurelegends.Assumptionsofnormalityandequalityofvariancewere autophagy,asalsoobservedearlyduringstarvation-inducedau- March2015 Volume35 Number6 MolecularandCellularBiology mcb.asm.org 959 Maetal. FIG 1BNIP3 expression results in transcriptional downregulation of autophagy-lysosome machinery. (A) Confocal images demonstrating LysoTracker fluorescence(top)andLAMP1expression(bottom)inNRCMstransducedwithBNIP3(green)orLacZ(24h),withorwithout3MA(7mmol/liter)andwith quantitation of the number of LAMP1-positive dots/nucleus. *, #, and $, P (cid:6) 0.05 versus LacZ, BNIP3, and BNIP3 plus 3MA, respectively. (B and C) Representativeflowcytometrictracings(B)andquantitation(C)ofLysoTrackerfluorescence(n(cid:8)3).*,P(cid:6)0.05versuscontrol(con)(whitebar).(DandE) Representativeimmunoblot(D)andquantitation(E)forLAMP1inNRCMstreatedasdescribedforpanelA(n(cid:8)3).*,P(cid:6)0.05versuscontrol(whitebar).(F toH)Representativeimmunoblot(aspreviouslydescribed[15])(F)andquantitationofLAMP1protein(n(cid:8)3)(G)andLAMP1transcripts(n(cid:8)4to6)(H)in NRCMs transduced with BNIP3 or LacZ for the indicated durations. (I) Levels of representative autophagy-lysosome machinery transcripts in NRCMs transducedwithBNIP3orLacZ(24h;n(cid:8)8).AlltransductionswereperformedatanMOIof100/sample. tophagy (18). However, BNIP3-induced declines in lysosome anism for induction of autophagosome formation (14), we abundance (assessed with the acidophilic dye LysoTracker Red examinedtheeffectofBNIP3expressiononbeclin-1.Beclin-1 [Fig.1AtoC]andbyimmunostainingforLAMP1[acandidate protein abundance was increased early (at 12 and 24 h) after lysosomalproteinwhoselevelsareusedtotracklysosomeabun- BNIP3 transduction (Fig. 2A and B), and this was not due to dance{35}][Fig.1A])andinLAMP1proteinabundance(Fig.1D transcriptionalinduction(Fig.2C).Infact,BECN1transcript andE)wereonlypartiallyrestoredwith3MA(atypeIIIphospha- levelsweresignificantlyreducedcomparedwiththoseofcon- tidylinositol 3-kinase inhibitor which inhibits autophagosome trols at 24 h, coinciding with the suppression of other au- formation)(Fig.1AtoE),to65%,59%,and72%,respectively,of tophagy-lysosome machinery transcripts (Fig. 1I), and only thelevelsforsimilarlytreatedcontrols.Thisindicatesthatlyso- increased subsequently, in parallel with a decline in beclin-1 some consumption in BNIP3-induced autophagy is only partly proteinabundance(Fig.2BandC)secondarytoconsumption responsiblefortheobserveddeclineinlysosomeabundance(15). withpersistentautophagy(datanotshown).Thissuggeststhat Importantly, we observed progressive declines in LAMP1 tran- a stabilization of beclin-1 protein results in its accumulation scripts(Fig.1H)parallelingthedeclineinLAMP1proteinabun- earlyafterBNIP3expression. dance(Fig.1FandG).Thistranscriptionalsuppressionalsoaf- We next examined if ROS mediate the BNIP3-induced in- fected multiple proteins (Fig. 1I) that participate in autophagy creaseinbeclin-1abundanceobservedwithreperfusioninjury (LC3, p62, and RAB7), constitute the lysosomes (LAMP2A, (6).BNIP3triggeredROSgenerationearlyafteritsexpression LAMP2B,cathepsinB,andcathepsinD),andfunctionasthemas- (at 12 h) (Fig. 2D and E), likely as a result of mitochondrial tertranscriptionalregulatoroftheautophagy-lysosomemachin- depolarization (Fig. 2F and G). Scavenging of ROS with ery(TFEB)butdidnotalterexpressionoftheunrelatedribosomal MnTMPyP,acell-permeatingsuperoxidedismutasemimetic, proteinsRPL32andRPS12(changesintranscript/GAPDHabun- dancesof0.95-(cid:10)0.02-fold[versus1.01-(cid:10)0.03-foldforLacZ] did not affect BNIP3-induced mitochondrial depolarization and0.95-(cid:10)0.03-fold[versus1.04-(cid:10)0.03-foldforLacZ],respec- (Fig. 2F and G) but prevented the increase in beclin-1 abun- tively; the P value was nonsignificant [NS]; n (cid:8) 8). Taken to- dance (Fig. 2H and I), indicating that BNIP3-induced mito- chondrialpermeabilizationisthecauseratherthantheconse- gether, these observations indicate that in contrast to the well- quenceofROSgeneration,whichprovokesincreasedbeclin-1 describedtranscriptionalstimulationoftheautophagy-lysosome machinery observed with starvation (21–24), BNIP3 expression abundance.TreatmentwithMnTMPyPinducedreductionsin resultsintranscriptionalsuppressionofthismachinerytoprevent LAMP1transcripts(Fig.2J)andproteinlevels(Fig.2KandL), itsreplenishment,whileautophagyisrobustlyinducedtoremove consistent with prior reports indicating that basal ROS levels BNIP3-damagedmitochondria(15). maydrivetranscriptionoflysosomalgenes(36).Importantly, We and others have observed a rapid increase in beclin-1 treatmentwithMnTMPyPpreventedBNIP3-induceddeclines abundance with reperfusion/reoxygenation injury (5, 6), and inLAMP1transcripts(Fig.2J)andprotein(Fig.2KandL)and elevated beclin-1 levels transcriptionally suppress autophagy- inlysosomes(Fig.2MandN)andattenuatedBNIP3-induced lysosomemachinerygenes(6).SinceBNIP3expressionispos- cardiomyocytedeath(Fig.2O).Takentogether,theseobserva- tulatedtodisplacebeclin-1fromitsbindingtoBcl2asamech- tions indicate that BNIP3-induced ROS mediate increased 960 mcb.asm.org MolecularandCellularBiology March2015 Volume35 Number6 Beclin-1RegulatesMitochondrialQualityviaTFEB FIG2BNIP3-inducedROSdriveincreasedbeclin-1proteinlevelsandsuppressionoflysosomeabundance.(AtoC)Representativeimmunoblot(A)and quantitationofbeclin-1protein(n(cid:8)3)(B)andBECN1transcripts(n(cid:8)3or4)(C)inNRCMstransducedwithBNIP3orLacZfortheindicateddurations.(D andE)Representativeflowcytometrictracings(D)andquantitation(E)ofROS(n(cid:8)3or4)inNRCMstransducedwithBNIP3orLacZfor12h.HO (500 2 2 mmol/liter;4h)wasusedasthepositivecontrol.(FandG)Representativeflowcytometrictracings(F)andquantitation(G)ofTMREfluorescence(n(cid:8)3)in NRCMstreatedasdescribedforpanelD.(HandI)Representativeimmunoblot(H)andquantitation(I)ofbeclin-1(n(cid:8)3or4)inNRCMstransducedwith BNIP3orLacZplusMnTMPyP(50(cid:5)mol/liter;24h).(JtoL)LAMP1transcript(n(cid:8)6)(J)andprotein(representativeimmunoblot[K]andquantitation[L] [n(cid:8)4])abundancesinNRCMstreatedasdescribedforpanelH.(MandN)Representativeflowcytometrictracings(M)andquantitation(N)ofLysoTracker fluorescence(n(cid:8)3).(O)CelldeathinNRCMstreatedasdescribedforpanelH(n(cid:8)7or8).AlltransductionswereperformedatanMOIof100/sample.*,P(cid:6) 0.05versuscontrol(whitebars). beclin-1abundanceandtheobservedtranscriptionalsuppres- therelativeabundanceofautolysosomesandreducedthelevelof sionofthelysosomemachinery. autophagosomes (versus the shLacZ control) in BNIP3-trans- Partialbeclin-1knockdowntranscriptionallystimulatesau- ducedNRCMs(Fig.3GandH),pointingtoenhancedautophagic tophagic flux to attenuate BNIP3-induced cardiomyocyte flux. Partial beclin-1 knockdown also resulted in an increased death. We have observed that experimental modulation of abundanceofautophagyproteins(totalLC3andp62)(Fig.3I), beclin-1levelstranscriptionallyaffectsautophagy-lysosomema- which was transcriptional as we described earlier (6; data not chinery proteins in a reciprocal fashion (6). To determine if shown),andinLAMP1(Fig.3IandJ),parallelingtheincreased BNIP3-induced upregulation of beclin-1 contributes to the ob- lysosome abundance. Importantly, partial beclin-1 knockdown serveddeclineinLAMP1,weperformedapartialknockdownof attenuatedtheBNIP3-induceddeclineinLAMP1protein(Fig.3I BECN1 transcripts (with two different shRNA constructs) in andJ),reducedBNIP3-inducedTUNELpositivity(Fig.3KandL), BNIP3(andLacZ)-treatedNRCMs.Partialbeclin-1knockdown and prevented BNIP3-induced cell death (Fig. 3M), mimicking (reductioninBECN1transcriptsto(cid:11)69%ofcontrollevelandin the observations seen with exogenous expression of TFEB (15). beclin-1proteinto(cid:11)45to50%ofcontrollevel)(Fig.3AtoC) Interestingly, partial beclin-1 knockdown resulted in reduced stimulated LAMP1 transcription (Fig. 3D) and increased lyso- BNIP3protein,whichwaspreventedbyconcomitantinhibition someabundance(Fig.3EandF)topreventBNIP3-inducedde- ofautophagosomeformationwith3MA(Fig.3N)butnotbypro- clines in lysosome numbers (Fig. 3E and F). BNIP3 expression teasome inhibition with MG-132, suggesting an enhanced au- resulted in autophagosome accumulation, indicating impaired tophagicdegradationofBNIP3togetherwiththemitochondria, autophagicflux(15),andpartialbeclin-1knockdownincreased whereupon it is localized. Partial beclin-1 knockdown with the March2015 Volume35 Number6 MolecularandCellularBiology mcb.asm.org 961 Maetal. 962 mcb.asm.org MolecularandCellularBiology March2015 Volume35 Number6 Beclin-1RegulatesMitochondrialQualityviaTFEB FIG4Nearlycompletebeclin-1knockdowninhibitsautophagytoincreaseBNIP3-inducedcelldeath.(A)BECN1transcriptlevelsinNRCMstransducedwith shBECN1-1,shBECN1-2,orshLacZ(MOI(cid:8)10;72h).(B)Representativeimmunoblot(top)andquantitation(bottom)ofbeclin-1proteinabundancein NRCMstreatedasdescribedforpanelA(n(cid:8)4).*,P(cid:6)0.05versusshLacZ.(CandD)GFP-taggedLC3localization(magnification,(cid:7)630;representativeof3 experiments)(C)andquantitationofpunctateGFP(D)inNRCMstreatedasdescribedforpanelAandcotransducedwithBNIP3orLacZ(24h)(n(cid:8)15to20 cells/group).*and#,P(cid:6)0.05versuscontrol(whitebars)andtheBNIP3-plus-shLacZgroup,respectively.(E)CelldeathinNRCMstreatedasdescribedforpanel C(n(cid:8)7to15).*,P(cid:6)0.05versuscontrol(whitebar). secondshRNAconstruct(shBECN1-2)(Fig.3AtoD)recapitu- Partial beclin-1 knockdown activates TFEB to attenuate latedthesefindings(datanotshown).Takentogether,thesedata BNIP3-inducedcardiomyocytedeath.Intriguingly,theeffectsof indicatethatpartialbeclin-1knockdowntranscriptionallystimu- partial beclin-1 knockdown (Fig. 3) mimicked our observa- latesautophagicfluxtorestoreimpairedautophagosomeprocess- tions with TFEB activation (15). Therefore, we evaluated the ingwithBNIP3expression. effect of partial beclin-1 knockdown on TFEB activation. Re- Notably, as we observed previously (6), a more complete centstudiesuncoveredatightlyregulatedmechanismforTFEB knockdownofBECN1(with10-foldhigheradenoviralshBECN1 activation, whereby TFEB is phosphorylated and sequestered transduction,to(cid:11)13%oftranscriptlevelswithshLacZ,resulting in the cytoplasm, in the unstressed state, and starvation-in- inareductionofbeclin-1proteinabundanceto(cid:11)7%ofthecon- duced mTOR inactivation provokes dephosphorylation and trollevel)(Fig.4AandB)resultedininhibitionofautophagosome nuclear translocation of TFEB (21, 22, 24). Given the lack of formation (Fig. 4C and D) and increased BNIP3-induced cell suitableantibodiestodetectendogenousTFEBinratcells(24), death (Fig. 4E), consistent with an obligate role for beclin-1 in weexaminedtheeffectofstarvationonsubcellulardistribution initiationofautophagy(26). ofexogenousTFEBinNRCMs.ExogenousTFEBexpressedat FIG3Partialbeclin-1knockdownstimulateslysosomebiogenesisandinducesautophagicfluxtoattenuateBNIP3-inducedcelldeath.(A)BECN1transcript levelsinNRCMstransducedwithtwoshBECN1constructsorshLacZ(MOI(cid:8)1;72h).(BandC)Representativeimmunoblot(B)andquantitation(C)of beclin-1protein(n(cid:8)4)inNRCMstreatedasdescribedforpanelA.*,P(cid:6)0.05versusshLacZ.(D)LAMP1transcriptlevelsinNRCMstreatedasdescribed forpanelAandcotransducedwithBNIP3orLacZ(MOI(cid:8)100;24h)(n(cid:8)4to12).*and#,P(cid:6)0.05versuscontrol(whitebar)andtherespective shBECN1-treatedgroup,respectively.(EandF)Representativeflowcytometrictracings(E)andquantitation(F)ofLysoTrackerfluorescenceinNRCMs transducedwithshBECN1-1orshLacZandcotransducedwithBNIP3orLacZasdescribedforpanelD(n(cid:8)3).(GandH)mCherry-GFP-LC3localization (magnification,(cid:7)630;representativeof3experiments)(G)andquantitationofautophagosomes,autolysosomes,andboth(H)inNRCMstreatedasdescribed forpanelB(n(cid:8)20to40nuclei/group).*,#,and$,P(cid:6)0.05forautophagosomes,autolysosomes,andboth,respectively,versusshLacZ-plus-LacZcontrol.(Iand J)Immunoblotdepictingautophagy-lysosomeproteins(I)andquantitationofLAMP1(n(cid:8)3)(J)inNRCMstreatedasdescribedforpanelE.*,P(cid:6)0.05versus control(whitebar).(KandL)Representativeimages(magnification,(cid:7)200)(K)andquantitationofTUNELpositivity(greeninpanelK)(n(cid:8)4)(L).(M)Cell deathinNRCMstreatedasdescribedforpanelE(n(cid:8)20to24).*,P(cid:6)0.05versuscontrol(whitebar).(N)BNIP3expressioninNRCMstransducedwith shBECN1-1orshLacZ(MOI(cid:8)1;72h)andcotransducedwithBNIP3orLacZ(MOI(cid:8)100;24h),withorwithout3MA(7mmol/liter)orMG-132(10 (cid:5)mol/liter). 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