PLANT ENDOSOMES : methods and protocols. PDF
Preview PLANT ENDOSOMES : methods and protocols.
Methods in Molecular Biology 2177 Marisa S. Otegui Editor Plant Endosomes Methods and Protocols Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Plant Endosomes Methods and Protocols Second Edition Edited by Marisa S. Otegui Department of Botany and Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA Editor MarisaS.Otegui DepartmentofBotanyandLaboratory ofCellandMolecularBiology UniversityofWisconsin-Madison Madison,WI,USA ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-0766-4 ISBN978-1-0716-0767-1 (eBook) https://doi.org/10.1007/978-1-0716-0767-1 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,orpartofthematerialisconcerned,specifically therightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproductiononmicrofilmsorinany otherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation,computersoftware,orby similarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLCpartofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface Endosomesarecriticalsortingorganellesinboththesecretoryandtheendocyticpathways. Twomaintypesofstructurallyandfunctionallydifferentendosomeshavebeendescribedin plants, the Trans Golgi Network (TGN) that acts as early endosome and mediates most of the recycling of endocytosed cargo back to the plasma membrane and the multivesicular endosomes, which sort endocytosed proteins into intraluminal vesicles for degradation at thevacuole.Newlysynthesizedsecretorycargoistransportedfromtheendoplasmicreticu- lumtotheGolgiandtheTGNforeithertheirdirectdeliverytotheplasmamembraneorto thevacuolethroughmultivesicularendosomes.Thus,endosomesarecriticalsortingstations of two important vesicle trafficking pathways. Understanding how endosomes and their associatedendosomalproteincomplexesdecodethesortingsignaturesoncargoandmedi- atemembranedeformationandvesiculationisunderactiveinvestigation. This second edition of Plant Endosomes: Methods and Protocols gathers a collection of techniquesto imagetrafficking ofcargo throughendosomes,tostudystructuralaspectsof plant endosomes by electron microscopy, and combined biochemical, omics, and imaging approaches to study the dynamics and contents of endosomal compartments. Finally, this edition also contains a group of chapters dedicated to the analysis of lipids on endosomes and the identification and analysis of lipid-binding proteins and lipid-binding domains relevantfor thestudyofplantendosomes. Iwouldliketoextendmymostsinceregratitudetoallauthorsandcolleaguesforhaving contributed detailed and useful protocols and great ideas to this book and to the National ScienceFoundationforsupportingresearchonendosomaltraffickinginmylaboratoryover theyears. Madison,WI,USA MarisaS.Otegui v Contents Preface ..................................................................... v Contributors................................................................. ix 1 AnalysisofEndocytosisandIntracellularTraffickingofBoric Acid/BorateTransportProteinsinArabidopsis............................. 1 AkiraYoshinariandJunpeiTakano 2 AnalysisofMembraneProteinsTransportfromEndosomal CompartmentstoVacuoles............................................... 15 MengqianLuo,YingZhu,ZhiqiLiu,andLiwenJiang 3 AnalysisofEndoplasmicReticulum–EndosomeAssociation UsingLive-CellImaginginPlantCells .................................... 23 GiovanniStefanoandFedericaBrandizzi 4 DegradationofAbscisicAcidReceptorsThroughtheEndosomalPathway..... 35 BorjaBelda-Palaz(cid:1)onandPedroL.Rodriguez 5 BiochemicalandImagingAnalysisofALIXFunction inEndosomalTraffickingofArabidopsisProteinCargoes.................... 49 MartaGarcı´a-Le(cid:1)onandVicenteRubio 6 CorrelativeLightandElectronMicroscopyImaging ofthePlanttrans-GolgiNetwork......................................... 59 PengfeiWangandByung-HoKang 7 ImagingPlantCellsbyHigh-PressureFreezingandSerial Block-FaceScanningElectronMicroscopy ................................. 69 KirkCzymmek,AbhilashSawant,KaijaGoodman,JanicePennington, PalPedersen,MrinaliniHoon,andMarisaS.Otegui 8 FunctionalAnalysisofPlantFYVEDomainProteins inEndosomalTrafficking ................................................ 83 WenjinShen,JuanWei,andCaijiGao 9 AssessingExtrinsicMembraneProteinDependencytoPI4P UsingaPlasmaMembranetoEndosomeRelocalizationTransient AssayinNicotianabenthamiana.......................................... 95 MehdiDoumaneandMarie-Ce´cileCaillaud 10 SubcellularLocalizationofPI3PinArabidopsis............................. 109 HanNimLee,HyeraJung,andTaijoonChung 11 ImmunopurificationofIntactEndosomalCompartments forLipidAnalysesinArabidopsis.......................................... 119 YokoIto,MagaliGrison,NicolasEsnay,LaetitiaFouillen,andYohann Boutte´ 12 Cell-FreeProteinTranslationSystemforExpressionofLipid-Binding ProteinsTaggedwithSmallEpitopesandTheirUse inProtein–LipidOverlayAssays .......................................... 143 JulioPaez-ValenciaandMarisaS.Otegui vii viii Contents 13 IsolationandGlycomicAnalysisofTrans-GolgiNetworkVesiclesinPlants .... 153 GuangxiRen,MichelRuizRosquete,AngeloG.Peralta,Sivakumar Pattathil,MichaelG.Hahn,ThomasWilkop,andGeorgiaDrakakaki 14 DetectionofPhosphorylationonImmunoprecipitatesfromTotal ProteinExtractsofArabidopsisthalianaSeedlings .......................... 169 KarinVogelandErikaIsono 15 PurificationandInteractionAnalysisofaPlant-SpecificRAB5 EffectorbyInVitroPull-DownAssay..................................... 183 EmiIto,Seung-wonChoi,andTakashiUeda Index ...................................................................... 199 Contributors BORJABELDA-PALAZO´N • InstitutodeBiologı´aMolecular yCelulardePlantas,Consejo SuperiordeInvestigacionesCientı´ficas-UniversidadPolite´cnicadeValencia,Valencia, Spain YOHANNBOUTTE´ • LaboratoiredeBiogene`seMembranaire,UMR5200,CNRS,Universite´ deBordeaux,Villenaved’Ornon,France FEDERICA BRANDIZZI • MSU-DOEPlantResearchLab,PlantBiologyDepartment, MichiganStateUniversity,EastLansing,MI,USA MARIE-CE´CILECAILLAUD • LaboratoireReproductionetDe´veloppementdesPlantes, Universite´deLyon,ENSdeLyon,UCBLyon1,CNRS,INRA,Lyon,France SEUNG-WON CHOI • DepartmentofNaturalSciences,InternationalChristianUniversity, Mitaka,Tokyo,Japan TAIJOONCHUNG • DepartmentofBiologicalSciences,PusanNationalUniversity,Busan, RepublicofKorea KIRKCZYMMEK • AdvancedBioimagingLaboratory,DonaldDanforthPlantScienceCenter, St.Louis,MO,USA MEHDIDOUMANE • LaboratoireReproductionetDe´veloppementdesPlantes,Universite´de Lyon,ENSdeLyon,UCBLyon1,CNRS,INRA,Lyon,France GEORGIADRAKAKAKI • DepartmentofPlantSciences,UniversityofCalifornia,Davis,CA, USA NICOLASESNAY • LaboratoiredeBiogene`seMembranaire,UMR5200,CNRS,Universite´de Bordeaux,Villenaved’Ornon,France;DepartmentofBiologicalSciences,BioDiscovery Institute,UniversityofNorthTexas,Denton,TX,USA LAETITIAFOUILLEN • LaboratoiredeBiogene`seMembranaire,UMR5200,CNRS,Universite´ deBordeaux,Villenaved’Ornon,France;MetaboHub-MetabolomeFacilityofBordeaux, FunctionalGenomicsCenter,Bordeaux,France CAIJIGAO • GuangdongProvincialKeyLaboratoryofBiotechnologyforPlantDevelopment, SchoolofLifeSciences,SouthChinaNormalUniversity,Guangzhou,China MARTAGARCI´A-LEO´N • CentroNacionaldeBiotecnologı´a(CNB-CSIC),Madrid,Spain KAIJAGOODMAN • DepartmentofBotany,UniversityofWisconsin-Madison,Madison,WI, USA;LaboratoryofCellandMolecularBiology,UniversityofWisconsin-Madison, Madison,WI,USA MAGALIGRISON • LaboratoiredeBiogene`seMembranaire,UMR5200,CNRS,Universite´de Bordeaux,Villenaved’Ornon,France MICHAELG.HAHN • ComplexCarbohydrateResearchCenter,UniversityofGeorgia,Athens, GA,USA MRINALINIHOON • DepartmentofOphthalmologyandVisualSciences,Universityof Wisconsin-Madison,Madison,WI,USA;McPhersonEyeResearchInstitute,Universityof Wisconsin-Madison,Madison,WI,USA ERIKAISONO • DepartmentofBiology,UniversityofKonstanz,Konstanz,Germany EMIITO • DepartmentofNaturalSciences,InternationalChristianUniversity,Tokyo, Japan;InstituteforGlobalLeadership,OchanomizuUniversity,Tokyo,Japan YOKOITO • LaboratoiredeBiogene`seMembranaire,UMR5200,CNRS,Universite´de Bordeaux,Villenaved’Ornon,France ix x Contributors LIWENJIANG • CentreforCell&DevelopmentalBiology,StateKeyLaboratoryof Agrobiotechnology,SchoolofLifeSciences,TheChineseUniversityofHongKong,Shatin, NewTerritories,HongKong,China HYERAJUNG • DepartmentofBiologicalSciences,PusanNationalUniversity,Busan, RepublicofKorea BYUNG-HOKANG • Center forCellandDevelopmentalBiology,StateKeyLaboratoryfor Agrobiotechnology,SchoolofLifeSciences,TheChineseUniversityofHongKong,Shatin, NewTerritories,HongKong,China HANNIMLEE • LaboratoryofCellandMolecularBiologyandDepartmentofBotany, UniversityofWisconsin-Madison,Madison,WI,USA ZHIQILIU • CentreforCell&DevelopmentalBiology,StateKeyLaboratoryof Agrobiotechnology,SchoolofLifeSciences,TheChineseUniversityofHongKong,Shatin, NewTerritories,HongKong,China MENGQIANLUO • CentreforCell&DevelopmentalBiology,StateKeyLaboratoryof Agrobiotechnology,SchoolofLifeSciences,TheChineseUniversityofHongKong,Shatin, NewTerritories,HongKong,China MARISAS.OTEGUI • DepartmentofBotany,UniversityofWisconsin-Madison,Madison,WI, USA;LaboratoryofCellandMolecularBiology,UniversityofWisconsin-Madison, Madison,WI,USA JULIO PAEZ-VALENCIA • LaboratoryofCellandMolecularBiology,UniversityofWisconsin- Madison,Madison,WI,USA SIVAKUMARPATTATHIL • ComplexCarbohydrateResearchCenter,UniversityofGeorgia, Athens,GA,USA;MascomaLLC(LallemandInc.),Lebanon,NH,USA PALPEDERSEN • CarlZeissMicroscopy,LLC,WhitePlains,NY,USA JANICE PENNINGTON • LaboratoryofCellandMolecularBiology,UniversityofWisconsin- Madison,Madison,WI,USA ANGELOG.PERALTA • ComplexCarbohydrateResearchCenter,UniversityofGeorgia, Athens,GA,USA GUANGXIREN • DepartmentofPlantSciences,UniversityofCalifornia,Davis,CA,USA; SchoolofChineseMateriaMedica,BeijingUniversityofChineseMedicine,Beijing,China PEDRO L.RODRIGUEZ • InstitutodeBiologı´aMolecular yCelulardePlantas,Consejo SuperiordeInvestigacionesCientı´ficas-UniversidadPolite´cnicadeValencia,Valencia, Spain MICHELRUIZROSQUETE • DepartmentofPlantSciences,UniversityofCalifornia,Davis, CA,USA;PlantBiologyLab.,SalkInstituteforBiologicalStudies,LaJolla,CA,USA VICENTE RUBIO • CentroNacionaldeBiotecnologı´a(CNB-CSIC),Madrid,Spain ABHILASHSAWANT • DepartmentofOphthalmologyandVisualSciences,Universityof Wisconsin-Madison,Madison,WI,USA;DepartmentofNeuroscience,Universityof Wisconsin-Madison,Madison,WI,USA WENJINSHEN • GuangdongProvincialKeyLaboratoryofBiotechnologyforPlant Development,SchoolofLifeSciences,SouthChinaNormalUniversity,Guangzhou,China GIOVANNISTEFANO • MSU-DOEPlantResearchLab,PlantBiologyDepartment,Michigan StateUniversity,EastLansing,MI,USA JUNPEI TAKANO • GraduateSchoolofLifeandEnvironmentalSciences,OsakaPrefecture University,Sakai,Osaka,Japan TAKASHIUEDA • DivisionofCellularDynamics,NationalInstituteforBasicBiology, Okazaki,Aichi,Japan;DepartmentofBasicBiology,SOKENDAI,Okazaki,Aichi,Japan KARINVOGEL • DepartmentofBiology,UniversityofKonstanz,Konstanz,Germany
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