MOLECULAR BIOWGY INTELLIGENCE UNIT Trafficking Inside Cells Pathways, Mechanisms and Regulation Nava Segev, PhD Department ofBiological Sciences Laboratoryfor Molecular Biology UniversityofIllinois at Chicago Chicago, Illinois, USA LANDES BIOSCIENCE SPRINGERSCIENCEtBuSINESSMEDIA AUSTIN, TEXAS NEW YORK,NEWYORK USA USA TRAFFICKING INSIDE CELLS: PATHWAYS, MECHANISMS AND REGULATION MolecularBiologyIntelligenceUnit LandesBioscience SpringerScience-BusinessMedia,LLC ISBN:978-0-387-93876-9 Printed onacid-freepaper. Copyright©2009LandesBioscienceand SpringerScience-BusinessMedia,LLC Allrights reserved. This work may not be translated or copied in whole or in part without the written permissionofthepublisher,exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysis.Usein connectionwith anyformofinformationstorageand retrieval,electronicadaptation,computersoftware,or bysimilarordissimilar methodologynowknown orhereafter developed isforbidden. 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SpringerScience-BusinessMedia,LLC,233 SpringStreet, NewYork,NewYork10013,USA http://www.springer.com Pleaseaddressallinquiriestothepublishers: LandesBioscience,1002WestAvenue,Austin,Texas78701,USA Phone:512/6376050; FAX:512/6376079 http://www.landesbioscience.com Thechapters inthisbookareavailableintheMadameCurieBioscienceDatabase. http://www.landesbioscience.com/curie PrintedinrheUnitedStatesofAmerica. 9 8 7 6 5 4 3 2 1 LibraryofCongress Cataloging-in-PublicationData Traffickinginsidecells:pathways, mechanisms,and regulation I [edited by]NavaSegev. p. ;ern.-- (Molecularbiologyintelligenceunit) Includesbibliographicalreferencesand index. ISBN 978-0-387-93876-9 (alk.paper) 1. Proteins--Physiologicaltransport. I.Segev,Nava.II. Series:Molecularbiologyintelligence unit(Unnumbered:2003) [DNLM:1. ProteinTransport.2. CellMembrane--metabolism.3. Cell Physiological Processes.4. SignalTransduction. QU55T7642009] QP551.T72352009 612.3'98--dc22 2009028590A Dedication Thisbookisdedicatedtoallthepast,presentandfutureresearchers whosecontributions areinvaluabletotherapidprogressionofthefield oftraffickinginsidethe cell. Nava Segev, PhD About theEditor... .... ... ,,.. '" NAVASEGEVisaProfessorin the DepartmentofBiologicalSciences at the UniversityofIllinoisatChicago. Herlaboratorystudies the regulation ofintracellular trafficking by GTPases using molecular, cellularand genetic approaches.Recently,her main researchinterestshavefocusedon the roleof GTPases in the integrationofindividualtransportstepsinto whole pathways andthecoordinationofthesepathwayswithothercellularprocesses.Sheteaches genetics to undergraduate students and protein trafficking to graduate students. Dr. Segevreceivedher PhD in Microbial Genetics from Tel-Aviv University in Israel and was a postdoctoral fellow with David Botstein at Massachusetts Institute ofTechnology, Cambridge, and Genentech, Inc. at San Francisco, where she picked up yeast asa model system. She currently serveson theEditorialBoardofMolecularBiologyoftheCell,andisamember ofthe GeneticSocietyofAmericaandtheAmericanSocietyforCellBiology. About the Associate Editors ... AIXA ALFONSO is an Associate Professor in the Department of BiologicalSciencesandtheLaboratoryfor IntegrativeNeuroscienceat the UniversityofIllinois at Chicago. Her research interests include thestudy ofthe genes involved in (1) sorting and trafficking of neuronal specific proteins (cell biology), and (2) specification ofneuronal identity (develop mentanddifferentiation) usingthe nematode C. elegansasamodelsystem. She received herPhDfrom theUniversityofWisconsinat Madisonandisa member ofthe Society for Neuroscience, the American Society for Cell Biology and the Society for the Advancement ofChicanos and Native Americans in Science. JULIE G.DONALDSON isa Senior Investigatorin the Laboratory ofCell Biology in the National Heart, Lung, and Blood Institute at the NationalInstitutesofHealthin Bethesda, Maryland.Herresearch interests arein understandingthe mechanismsandregulationofendosomalandsecre tory membrane traffic in the cell. She holds a PhD from the Universityof MarylandandwasaPostdoctoral Fellow in theNational InstituteofChild Healthand Human Developmentpriorto hercurrentposition. GREGORYS.PAYNE isa Professor in the Department ofBiological Chemistry, UCLASchool ofMedicine,LosAngeles, California.His research involves cell biological, biochemical, molecular and standard genetic and genomic approaches to understand vesicle mediated traffic in yeast, with particular emphasis on endocytosis and transport between theTGN and endosomes.Dr. PaynereceivedhisBSinCell BiologywithHonorsinDrama from UniversityofMichiganin 1977andhisPhDin Biochemistryinthelab ofHaroldVarmus from UniversityofCalifornia, San Francisco. Hewas apostdoctoralfellowwith RandySchekman at UniversityofCalifornia, Berkeley.Hecurrentlyserveson theEditorialBoardsofTrafficandtheJournal ofCellScienceandisamemberoftheAmericanSocietyofCell Biology. CONTENTS r;:::::::::::============= ============:::::::=;"] Preface ......•........................................................•................•..............•xix NavaSegev Section I. Compartments and Pathways 1. OverviewofIntracellularCompartments and TraffickingPathways 3 AndreiA. Tokareo, AixaAlfonsoandNauaSegeu Abstract 3 Introduction 4 How We Study IntracellularTrafficking 5 TheExocyricPathway 6 TheEndocytic Pathway 7 Cross-Talk betweenthe Exocyricand Endocytic Pathways 7 RegulatedTrafficking 9 CompartmentDynamics and Biogenesis 12 Summaryand FuturePerspectives 12 2. HowWe StudyProteinTransport 15 Mary1.Preuss,PeggyWeidmanandErikNielsen Abstract............................................................................................... 15 Model Cargo Proteins fortheAnalysis ofIntracellular Transport 16 TheReconstitutionofMembraneTraffickingInVitro 19 GeneticAnalysisofTransportinYeast 25 Tools forImaging MembraneTrafficking 30 Summaryand Perspectives 34 3. TheGolgiApparatus 42 ZhaolinHuaandToddR Graham Abstract 42 Introduction 43 Structureofthe GolgiApparatus 44 PosttranslationalModifications Catalyzedwithin the Golgi Apparatus 48 Protein Transportand Sortingin the GolgiApparatus 54 Inheritanceofthe GolgiApparatus 60 Summary 61 4. TheEndocyticPathway ....................................................•..................67 Elizabeth ConibearandYuen YiC. Tam Abstract 67 Initial Stepsin Internalization 68 TransportthroughEndosomes 71 RetrogradeTransportto the SecretoryPathway 74 MembraneDomainsand CompartmentIdentity 77 Conclusion 77 5. RegulatedSecretion................................•.............................................84 NaueenNagarajan, KennethL. CusterandSandraBajjalieh Abstract 85 Introduction 85 Adapting theCoreMachineryofConstitutiveSecretion forRegulatedRelease 85 Adding Regulationto theCoreMachinery 88 SecretionatNeuronal Synapses 93 Summaryand Conclusion 95 Section II. Mechanisms 6. OverviewofProteinTraffickingMechanisms 105 Giancarlo CostagutaandGregoryS.Payne Abstract............................................................................................. 105 Introduction 105 Translocationand Protein Foldinginthe ER 108 Coated VesicleFormation 109 Dense CoreSecretoryGranule Formation 111 Carrier Motility and OrganellePositioning 112 VesicleTetheringand Fusion 113 RoleofLipidsinProtein Trafficking 114 Summary 115 7. Entryinto the EndoplasmicReticulum: ProteinTranslocation, Foldingand QualityControl 119 Sbeara "Iv. FewellandJeffreyL.Brodsky Abstract............................................................................................. 119 Introduction 119 ProteinTranslocationacrossthe ERMembrane 120 QualityControlinthe ER 128 The Unfolded Protein Response(UPR) 131 ERand HumanHealth 131 ConcludingRemarks 133 8. COP-MediatedVesicleTransport 143 SiloerePagantandElizabethMiller Abstract.......................................................................... 143 Introduction: PrinciplesofVesicularTraffic 144 InitiatingVesicleFormation:AGTPase CycleRegulates Coat Assembly 144 Sculpting the Membrane:Generatingand Capturing MembraneCurvature 148 PopulatingtheVesicle:Cargo-CoatInteractions Specify EfficientCargoCapture 150 ComplexityinCOP-MediatedTraffic:WhatRemains ToBeLearned 152 Conclusion 155 9. Clathrin-MediatedEndocytosis 159 PeterS.McPherson, BrigitteRitterandBeverlyWendland Abstract 159 Introduction 160 Mechanisms ofCCVFormation 162 Actin 173 Major UnresolvedQuestions 175 10. BiogenesisofDense-CoreSecretoryGranules 183 GrantR Bowman,AndrewT.CowanandAaronP. Turkewitz Abstract............................................ 183 Introduction 184 ProteinSortinginto ISGs 187 VesicleBuddingand Maturation 195 Conclusion 201 11. Lipid-DependentMembraneRemodelling in ProteinTrafficking 210 PriyaP. ChandraandNicholas T.Ktistakis Abstract 210 Introductionand Overview 211 TransportPathways 211 Coated VesicleFormationPrimarilyDependsonThreeTypes ofCoats: Clathrin; COPIIand COPI 213 Structuraland SignalingLipidsinMembraneTransport 215 EvidenceThatLipidsRegulateTrafficking Pathways 218 HowDoesItWork?SomeEmerging Principles 222 FutureDirections 227 12. CarrierMotility 233 MarcinJ WozniakandVictoriaJ Allan Abstract 233 Introduction 233 Microtubulesand TheirMotors 235 Actin FilamentsandTheirMotors 237 Tothe Golgiand Back-TheEarlySecretoryPathway 240 TGNand Post-GolgiTrafficking 242 Endocytosis 244 CooperationbetweenMotorProteins 247 FuturePerspectives 247 13. TetheringFactors 254 VladimirLupasbinandElizabethSztul Abstract 254 Introduction 255 RoleofCoiled-Coil TethersinMembraneTraffic 256 RoleofMulti-SubunitTetheringComplexesin MembraneTraffic 261 UnconfirmedTethers 266 ModelsforFunctionofTetheringProteinsin MembraneTraffic 268 Conclusionand Perspectives 272 14. IntracellularMembraneFusion 282 DaluXuandJesse C Hay Abstract 283 Fusion ofPhospholipid Bilayers:BiophysicalMechanism 283 General Mechanisms ofProtein-AssistedMembraneFusion 284 MembraneFusion ofEnvelopedViruses 284 Intracellular MembraneFusion 287 Calcium-Activated MembraneFusion 308 Perspectives 311 Section III. Regulation and Coordination withOther Cellular Processes 15. Regulationand CoordinationofIntracellularTrafficking: An Overview 329 JulieDonaldsonandNavaSegev Abstract 329 Introduction 330 Regulation ofIndividuaiTransportSteps 330 Transport StepCoordination 333 Coordination ofIntracellularTraffickingwith Other Cellular Processes 334 TrafficRegulation and HumanDisease 337 FuturePerspectives 338 16. RegulationofProteinTraffickingbyGTP-BindingProteins 342 MichelFranco, PhilippeChavrierandFlorenceNiedergang Abstract 342 Introduction 343 SmallGTP Binding Proteins:General Properties and MechanismsofRegulation 343 Methodsto Study GTP-BindingProteins 347 Rolein Protein Trafficking 349 ConcludingRemarks 357