PLANT ENDOSOMES : methods and protocols.

203 Pages·2020·6.031 MB·English

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
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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
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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