Endosome Signaling Part A PDF
Preview Endosome Signaling Part A
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON and MELVIN I. SIMON Division of Biology California Institute of Technology Pasadena, California ANNA MARIE PYLE Departments of Molecular, Cellular and Developmental Biology and Department of Chemistry Investigator, Howard Hughes Medical Institute Yale University GREGORY L. VERDINE Department of Chemistry and Chemical Biology Harvard University Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 225WymanStreet,Waltham,MA02451,USA Radarweg29,POBox211,1000AEAmsterdam,TheNetherlands TheBoulevard,LangfordLane,Kidlington,Oxford,OX51GB,UK 32JamestownRoad,LondonNW17BY,UK Firstedition2014 Copyright©2014ElsevierInc.AllRightsReserved. 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Becauseofrapidadvancesinthemedicalsciences,inparticular,independentverificationof diagnosesanddrugdosagesshouldbemade ForinformationonallAcademicPresspublications visitourwebsiteatstore.elsevier.com ISBN:978-0-12-397926-1 ISSN:0076-6879 PrintedandboundinUnitedStatesofAmerica 14 15 16 17 11 10 9 8 7 6 5 4 3 2 1 CONTRIBUTORS MihaelaAnitei BiotechnologyCenter,DresdenUniversityofTechnology,Dresden,Germany SpyrosArtavanis-Tsakonas DepartmentofCellBiology,HarvardMedicalSchool,Boston,Massachusetts,USA YorikoAtomi GraduateSchoolofInformationScienceandTechnology,andRadioisotopeCenter,Cellto BodyDynamicsLaboratory1,TheUniversityofTokyo,Tokyo,Japan NicolasF.Berbari DepartmentofCell,DevelopmentalandIntegrativeBiology,UniversityofAlabamaat Birmingham,Birmingham,Alabama,USA LeanneBilawchuk LiKaShingInstituteofVirology,DepartmentofMedicalMicrobiologyandImmunology, UniversityofAlberta,Edmonton,Alberta,Canada JohanneBouthillier Centrederechercheenrhumatologieetimmunologie,CentreHospitalierUniversitairede Que´bec,Que´bec,Canada AndreasBrech CentreforCancerBiomedicine,FacultyofMedicine,UniversityofOslo,andInstitutefor CancerResearch,TheNorwegianRadiumHospital,OsloUniversityHospital,Oslo, Norway SophiaY.Breusegem DepartmentofClinicalBiochemistry,CambridgeInstituteforMedicalResearch,University ofCambridge,Addenbrooke’sHospital,Cambridge,UnitedKingdom JorgeCancino DepartmentofLifeSciences,InstituteofProteinBiochemistry,NationalResearchCouncil andTelethonInstituteofGeneticsandMedicine,Naples,Italy C.YanCheng TheMaryM.WohlfordLaboratoryforMaleContraceptiveResearch,Centerfor BiomedicalResearch,PopulationCouncil,NewYork,USA BrettM.Collins InstituteforMolecularBioscience,UniversityofQueensland,St.Lucia,Queensland, Australia EmmanuelCuletto CentredeGe´ne´tiqueMole´culaire,CNRSUPR3404,Universite´ Paris-Sud,91198 Gif-sur-YvetteCedex,France xiii xiv Contributors ManlioDiCristina DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy CarlaEmiliani DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy MitsunoriFukuda LaboratoryofMembraneTraffickingMechanisms,DepartmentofDevelopmentalBiology andNeurosciences,GraduateSchoolofLifeSciences,TohokuUniversity,Sendai,Miyagi, Japan EmiliaGalperin DepartmentofMolecularandCellularBiochemistry,UniversityofKentucky,Lexington, Kentucky,USA RajeshGhai InstituteforMolecularBioscience,UniversityofQueensland,St.Lucia,Queensland,Australia MonicaGiannotta FIRCInstituteofMolecularOncologyFoundation,Milan,Italy JenniferM.Gillette DepartmentofPathology,UniversityofNewMexicoHealthSciencesCenter, Albuquerque,NewMexico,USA MarcosGonza´lez-Gaita´n DepartmentofBiochemistry,FacultyofSciences,andDepartmentofMolecularBiology, FacultyofSciences,GenevaUniversity,Geneva,Switzerland RichardG.Hegele DepartmentofLaboratoryMedicineandPathobiology,UniversityofToronto,Toronto, Ontario,Canada BernardHoflack BiotechnologyCenter,DresdenUniversityofTechnology,Dresden,Germany KazuyaHori DepartmentofCellBiology,HarvardMedicalSchool,Boston,Massachusetts,USA MyoungkunJeoung DepartmentofMolecularandCellularBiochemistry,UniversityofKentucky,Lexington, Kentucky,USA TaihoKambe GraduateSchoolofBiostudies,KyotoUniversity,Kyoto,Japan ChristopheLefebvre CentredeGe´ne´tiqueMole´culaire,CNRSUPR3404,Universite´Paris-Sud,91198Gif-sur- YvetteCedex,France RenaudLegouis CentredeGe´ne´tiqueMole´culaire,CNRSUPR3404,Universite´Paris-Sud,91198Gif-sur- YvetteCedex,France Contributors xv GuyM.Lenk DepartmentofHumanGenetics,UniversityofMichigan,AnnArbor,Michigan,USA PearlP.Y.Lie TheMaryM.WohlfordLaboratoryforMaleContraceptiveResearch,Centerfor BiomedicalResearch,PopulationCouncil,NewYork,USA SylvainLoube´ry DepartmentofBiochemistry,FacultyofSciences,andDepartmentofMolecularBiology, FacultyofSciences,GenevaUniversity,Geneva,Switzerland AlessandroMagini DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy MarionManil-Se´galen CentredeGe´ne´tiqueMole´culaire,CNRSUPR3404,Universite´Paris-Sud,91198Gif-sur- YvetteCedex,France RobertaMannucci IMAGEAnalysisLaboratory,UniversityofPerugia,Perugia,Italy Franc¸oisMarceau Centrederechercheenrhumatologieetimmunologie,CentreHospitalierUniversitairede Que´bec,Que´bec,Canada DavidJ.Marchant LiKaShingInstituteofVirology,DepartmentofMedicalMicrobiologyandImmunology, UniversityofAlberta,Edmonton,Alberta,Canada KristopherD.Marjon DepartmentofPathology,UniversityofNewMexicoHealthSciencesCenter, Albuquerque,NewMexico,USA TakahideMatsui LaboratoryofMembraneTraffickingMechanisms,DepartmentofDevelopmentalBiology andNeurosciences,GraduateSchoolofLifeSciences,TohokuUniversity,Sendai,Miyagi, Japan MiriamH.Meisler DepartmentofHumanGenetics,UniversityofMichigan,AnnArbor,Michigan,USA MehdiMobli CentreforAdvancedImaging&SchoolofChemistryandMolecularBiosciences, TheUniversityofQueensland,St.Lucia,Queensland,Australia DoloresD.Mruk TheMaryM.WohlfordLaboratoryforMaleContraceptiveResearch,Centerfor BiomedicalResearch,PopulationCouncil,NewYork,USA IldoNicoletti IMAGEAnalysisLaboratory,UniversityofPerugia,Perugia,Italy ChristianNiehage BiotechnologyCenter,DresdenUniversityofTechnology,Dresden,Germany xvi Contributors GordonNish LiKaShingInstituteofVirology,DepartmentofMedicalMicrobiologyandImmunology, UniversityofAlberta,Edmonton,Alberta,Canada AsamiOguro-Ando DepartmentofNeuroscienceandPharmacology,RudolfMagnusInstituteofNeuroscience, UniversityMedicalCentreUtrecht,Utrecht,TheNetherlands EriOhoto-Fujita GraduateSchoolofInformationScienceandTechnology,andRadioisotopeCenter,Cellto BodyDynamicsLaboratory1,TheUniversityofTokyo,Tokyo,Japan AlicePolchi DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy CarolineRoy Centrederechercheenrhumatologieetimmunologie,CentreHospitalierUniversitairede Que´bec,Que´bec,Canada CarmenRuggiero DepartmentofCellularandTranslationalPharmacology,FondazioneMarioNegriSud,Unit ofGenomicApproachestoMembraneTraffic,SantaMariaImbaro(CH),Italy MicheleSallese DepartmentofCellularandTranslationalPharmacology,FondazioneMarioNegriSud,Unit ofGenomicApproachestoMembraneTraffic,SantaMariaImbaro(CH),Italy KayOliverSchink CentreforCancerBiomedicine,FacultyofMedicine,UniversityofOslo,andInstitute forCancerResearch,TheNorwegianRadiumHospital,OsloUniversityHospital, Oslo,Norway MatthewN.J.Seaman DepartmentofClinicalBiochemistry,CambridgeInstituteforMedicalResearch,University ofCambridge,Addenbrooke’sHospital,Cambridge,UnitedKingdom AnindyaSen DepartmentofCellBiology,HarvardMedicalSchool,Boston,Massachusetts,USA MihoShimizu GraduateSchoolofInformationScienceandTechnology,andRadioisotopeCenter,Cellto BodyDynamicsLaboratory1,TheUniversityofTokyo,Tokyo,Japan ChristophStange BiotechnologyCenter,DresdenUniversityofTechnology,Dresden,Germany HaraldStenmark CentreforCancerBiomedicine,FacultyofMedicine,UniversityofOslo,andInstitute forCancerResearch,TheNorwegianRadiumHospital,OsloUniversityHospital, Oslo,Norway MelanieL.Styers DepartmentofBiology,Birmingham-SouthernCollege,Birmingham,Alabama,USA Contributors xvii ElizabethSztul DepartmentofCell,DevelopmentalandIntegrativeBiology,UniversityofAlabamaat Birmingham,Birmingham,Alabama,USA BrunellaTancini DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy CristyTower-Gilchrist DepartmentofCellBiology,EmoryUniversity,Atlanta,Georgia,USA LorenaUrbanelli DepartmentofExperimentalMedicineandBiochemicalSciences,SectionofBiochemistry andMolecularBiology,UniversityofPerugia,Perugia,Italy CatherineSemWegner CentreforCancerBiomedicine,FacultyofMedicine,UniversityofOslo,and InstituteforCancerResearch,TheNorwegianRadiumHospital,OsloUniversity Hospital,Oslo,Norway ChrisK.C.Wong DepartmentofBiology,HongKongBaptistUniversity,HongKong,China ElissaW.P.Wong TheMaryM.WohlfordLaboratoryforMaleContraceptiveResearch,Centerfor BiomedicalResearch,PopulationCouncil,NewYork,USA XiangXiao TheMaryM.WohlfordLaboratoryforMaleContraceptiveResearch,Centerfor BiomedicalResearch,PopulationCouncil,NewYork,USA,andDepartmentof ReproductivePhysiology,ZhejiangAcademyofMedicalSciences,Hangzhou, Zhejiang,China BradleyK.Yoder DepartmentofCell,DevelopmentalandIntegrativeBiology,UniversityofAlabamaat Birmingham,Birmingham,Alabama,USA PREFACE Endosomesaremembrane-boundcompartmentsthattransportinternalized material from the plasma membrane to the lysosome and elsewhere.These compartments,oftenabout500nm,butranginginsize,havethecapability to sort molecules, routing some contents to the lysosomes for degradation, and recycling other materials back to the plasma membrane. The Golgi apparatus also provides molecules to the endosome, some of which are delivered to lysosomes and others are recycled back to the Golgi. Because of this ability to differentially deliver molecules, the endosome is viewed as a presorting structure. Endosomesarecategorizedbysize,enzymaticcontent,morphology,and by other criteria such as the length of time it takes internalized material to reach them. Endosomes may provide platforms for cross talk between sig- nalingsystems,andthisconsiderationhasprovidedthemelitestatusamong cellular components that contribute to signaling. Thisvolumeprovidesdescriptionsoftherangeofmethodsusedtoana- lyzeandevaluatetheseimportantcompartments.Theauthorsexplainhow these methodsareabletoprovideimportantbiological insights inthecon- text of particular models. Authorswereselectedbasedonboththeirresearchcontributionsandon their ability to describe their methodological contributions in a clear and reproducible way. They have been encouraged to make use of graphics, comparisons to other methods, and to provide tricks and approaches not revealed in prior publications that make it possible to adapt their methods to other systems. Theeditorwantstoexpressappreciationtothecontributorsforprovid- ingtheircontributionsinatimelyfashion,tothesenioreditorsforguidance, and to the staff at Academic Press for helpful input. P. MICHAEL CONN Lubbock, TX, USA xix CHAPTER ONE Monitoring Phosphatidylinositol 3-Phosphate in Multivesicular Endosome Biogenesis Catherine Sem Wegner*,†, Kay Oliver Schink*,†, Harald Stenmark*,†, Andreas Brech*,†,1 * CentreforCancerBiomedicine,FacultyofMedicine,UniversityofOslo,Oslo,Norway †InstituteforCancerResearch,TheNorwegianRadiumHospital,OsloUniversityHospital,Oslo,Norway 1Correspondingauthor:e-mailaddress:[email protected] Contents 1. Introduction 4 2. LocalizationofPtdIns3PandEGFR 5 2.1 PtdIns3PandEGFRlocalizationbyconfocalmicroscopy 7 2.2 PtdIns3PandEGFRlocalizationbysuper-resolutionlightmicroscopy 9 2.3 PtdIns3PandEGFRlocalizationbyimmuno-EM 10 2.4 PtdIns3Plocalizationbypre-embeddingimmuno-EM 13 3. CorrelativeLightandElectronMicroscopyofMVEs 16 3.1 Seedingofcellsongriddedcoverslips 17 3.2 Fixation,staining,andmounting 18 3.3 Observationofcellswithlightmicroscopyandregistrationofcellposition 18 3.4 Eponembedding,locatingregisteredcells,andserialsectioning 19 3.5 Electronmicroscopy 21 3.6 Correlationandimageprocessing 21 4. ConcludingRemarks 21 Acknowledgments 22 References 22 Abstract Theendocyticpathwaycomprisesavarietyofintracellularcompartmentsthatregulate sortingofinternalizedplasmamembraneconstituentsaswellasextracellularmaterial. Amajorsortingstationonthisrouteistheearlyendosome,whereinternalizedreceptors destinedfordegradationaretraffickedfromthelimitingmembraneintotheinteriorof theendosomebyformationofintraluminalvesicles(ILVs).Thisinvaginationandbud- dingprocessleadstothebiogenesisofmultivesicularendosomes(MVEs).Theformation ofILVsdependsonthesequentialactionofproteincomplexesthatarepartlyrecruited in a phosphatidylinositol 3-phosphate (PtdIns3P)-dependent manner.The underlying mechanisms of the biogenesis of MVEs are still not completely understood and it is MethodsinEnzymology,Volume534 #2014ElsevierInc. 3 ISSN0076-6879 Allrightsreserved. http://dx.doi.org/10.1016/B978-0-12-397926-1.00001-9 4 CatherineSemWegneretal. therefore of great interest to study the sorting of PtdIns3P in this process. We are describing several methods to track these sorting events by both light and electron microscopyandcombinationofbothmethods. 1. INTRODUCTION Multivesicular endosomes (MVEs) are important organelles in the endocytic pathway where they serve to regulate signaling through sorting and subsequent lysosomal degradation of receptors and their ligand (Gruenberg & Stenmark, 2004). Receptors such as the epidermal growth factor receptor (EGFR) are sorted into intraluminal vesicles (ILVs) of the MVEandthereafterdegradeduponfusionwiththelysosome.Thecharged phospholipid phosphatidylinositol 3-phosphate(PtdIns3P) hasbeen shown to be necessary for the formation of ILVs (Futter, Collinson, Backer, & Hopkins,2001).PtdIns3Pisfoundintheendocyticpathwayandmostabun- dantly on early endosomes (EEs) and internal vesicles of MVEs (Gillooly et al., 2000). PtdIns3P generated on EEs can be further phosphorylated to produce phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P ], which is 2 thought to reside predominantly on late endosomes (De Matteis & Godi, 2004). Effectors of PtdIns3P directly bind the phospholipid, mostly via one of two PtdIns3P-binding domains, the FYVE domain (Burd & Emr, 1998; Gaullier et al., 1998; Patki, Lawe, Corvera, Virbasius, & Chawla, 1998; Raiborg, Schink, & Stenmark, 2013) or the PX (Phox homology) domain (Simonsen & Stenmark, 2001). The FYVE domain is the only phosphoinositide-binding domain found so far to only bind a single pho- sphoinositide (namely, PtdIns3P) (De Matteis & Godi, 2004). The FYVE domain is also the smallest of the phosphoinositide-binding domains and the one with the highest sequence conservation (Simonsen & Stenmark, 2001).SeveraloftheFYVEdomain-containingproteinsareinvolvedinves- icle trafficking, signal transduction, and cytoskeletal functions. AfunctionoftheFYVEdomainwasfirstsuggestedwhenitwasfoundto be responsible for targeting early endosomal antigen1 (EEA1) to the EE (Stenmark, Aasland, Toh, & D’Arrigo, 1996). EEA1 has later been shown to be recruited to the EE by PtdIns3P and the small GTPase Rab5. Here EEA1actsonhomo-andheterotypicfusionofendosomes.Otherproteins localizingtotheendosomalpathwayhavealsobeenshowntocontainFYVE
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