Plasmodesmata: Methods and Protocols

465 Pages·2022·14.566 MB·English

by  Yoselin Benitez-Alfonso, Manfred Heinlein

Methods in
Molecular Biology 2457
Yoselin Benitez-Alfonso
Manfred Heinlein Editors
Plasmodesmata
Methods and Protocols
Second Edition
M M B
ETHODS IN OLECULAR IO LO GY
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School of Lifeand MedicalSciences
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Plasmodesmata
Methods and Protocols
Second Edition
Edited by
Yoselin Benitez-Alfonso
Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, UK
Manfred Heinlein
Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
Editors
YoselinBenitez-Alfonso ManfredHeinlein
CentreforPlantSciences,Schoolof InstitutdeBiologieMole´culairedesPlantes,CNRS
Biology Universite´deStrasbourg
UniversityofLeeds Strasbourg,France
Leeds,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2131-8 ISBN978-1-0716-2132-5 (eBook)
https://doi.org/10.1007/978-1-0716-2132-5
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Preface
Plasmodesmata, the nanochannels that connect plant cells, are crucial for intercellular
signaling by playing a key role in plant development and response to the environment.
Research on plasmodesmata structure and regulation is growing as accumulating evidence
relatesthefunctionofthesechannelstocropyieldaswellasresiliencetoclimatechangeand
devastating diseases. Despite their importance, we are still far from being able to translate
knowledge on plasmodesmata structure and function into the design of strategies to
improve food security. This is partly due to the lack of tools and resources to study these
channels and to enable their targeted modification. Nevertheless, thefield hasmade major
advancesinbothmethodologyandcurrentknowledge.
Thus, following the first edition of Plasmodesmata: Methods and Protocols published in
2015,itbecametimetocreateasecondedition,whichcompilesnew,up-to-dateprotocols,
writtenbyexpertsinthefieldofplasmodesmataresearch.Theaimistofacilitatethestudyof
these structures and to instigate new research that will further advance our knowledge on
plasmodesmata in labs around the world. Plasmodesmata research was classically driven by
cell biologists, but in recent years we acknowledge the significant contribution of other
disciplinesincludingbiochemistry,molecularbiology,andmathematicalmodeling.Conse-
quently, protocols in the book expand to a broad range of disciplines suitable for studying
plasmodesmatafrommultipleangles.
The book is divided into five parts: the first part contains two reviews addressing the
general structural composition and regulation of plasmodesmata as well as discussing their
role in plant development and disease. The second part is dedicated to methods to study
plasmodesmata architectures and distribution in cell interfaces, including the most recent
advancesinpreparingandimagingtheplantmaterialusingelectrontomographyandhigh-
resolution microscopy. The third part focuses on approaches to dissect plasmodesmata
composition, specially targeting callose accumulation and membranes lipidomic and pro-
teomic analysis as well as methods to study protein clustering and membrane organization
around plasmodesmata. The fourth part collects protocols to quantify changes in plasmo-
desmata permeability using fluorescent tracers and mobile proteins. This section also con-
tainstoolstointerrogateplasmodesmatafunctionusingvectorsforcalloseinductionanda
forward genetic screen to identify trafficking regulators. To conclude, we included a fifth
partwithprotocolsthatcontributetoplasmodesmataresearchbutfalloutsidetheprevious
classifications. These are tools to visualize mobile RNAs, to image cell interfaces in the
meristem, and to measure/predict symplasmic connectivity using modeling and computa-
tionalapproaches.
We,theeditors,believethiscompendiumwillbeusefultoallplantscientists,especially
those studying cell-to-cell communication pathways. We have worked with the authors to
make the protocols accessible to beginners and experts; thus the book will be useful for
advanced researchers as well as for the teaching and training of young scientists. We hope
thatthisbookwillbecomeamajor resourceinthelaboratories.
Leeds,UK YoselinBenitez-Alfonso
Strasbourg,France Manfred Heinlein
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I OVERVIEWARTICLES
1 PlasmodesmataStructuralComponentsandTheirRoleinSignaling
andPlantDevelopment.................................................. 3
PhilipKirkandYoselinBenitez-Alfonso
2 FunctionofPlasmodesmataintheInteractionofPlants
withMicrobesandViruses............................................... 23
CaipingHuangandManfredHeinlein
PART II STRUCTURE AND DISTRIBUTION OF PLASMODESMATA
3 PlasmodesmataUltrastructureDeterminationUsingElectron
Tomography ........................................................... 57
JulesD.Petit,MarieGlavier,LysianeBrocard,
andEmmanuelleM.F.Bayer
4 UltrastructuralAnalysisandThree-DimensionalReconstruction
ofPlasmodesmata....................................................... 75
KamilaGodel-Je˛drychowska,TilmanFranke,andEwaKurczyn´ska
5 SerialBlockElectronMicroscopytoStudyPlasmodesmata
intheVasculatureofArabidopsisthalianaRoots............................ 95
AndreaPaterliniandIlyaBelevich
6 FocusedIonBeam-ScanningElectronMicroscopyforInvestigating
PlasmodesmalDensities.................................................. 109
BrandonC.Reagan,JohnR.Dunlap,andTessaM.Burch-Smith
7 MeasuringPlasmodesmataDensityonCellInterfacesofMonocot
LeavesUsing3DImmunolocalizationandScanningElectron
Microscopy............................................................. 125
FlorenceR.Danila
8 Super-ResolutionImagingofPlasmodesmataUsing3DStructured
IlluminationMicroscopy................................................. 143
KirstenKnox
PART III COMPOSITIONAL ANALYSIS OF PLASMODESMATA
9 InVivoAnilineBlueStainingandSemiautomatedQuantification
ofCalloseDepositionatPlasmodesmata................................... 151
CaipingHuang,JeroˆmeMutterer,andManfred Heinlein
10 ImmunofluorescenceDetectionofCalloseinPlantTissueSections ........... 167
SamAmsburyandYoselinBenitez-Alfonso
vii
viii Contents
11 CalloseDetectionandQuantificationatPlasmodesmatainBryophytes........ 177
ArthurMuller,TomomichiFujita,andYoanCoudert
12 IsolationofPlasmodesmataMembranesforLipidomicandProteomic
Analysis................................................................ 189
LaetitiaFouillen,Ste´phaneClaverol,EmmanuelleM.F.Bayer,
andMagaliS.Grison
13 MethodsforDetectionofProteinInteractionswithPlasmodesmata-
LocalizedReticulons .................................................... 209
VerenaKriechbaumerandStanleyW.Botchway
14 StudyingProtein–ProteinInteractionsatPlasmodesmatabyMeasuring
Fo¨rsterResonanceEnergyTransfer ....................................... 219
PatrickBlu¨mke,VickyHowe,andRu¨digerSimon
15 QuantifyingtheOrganizationandDynamicsofthePlantPlasma
MembraneAcrossScalesUsingLightMicroscopy .......................... 233
JosephF.McKenna
16 UsingSteady-StateFluorescenceAnisotropytoStudyProteinClustering...... 253
AjeetChaudharyandKaySchneitz
PART IV FUNCTIONAL ANALYSIS OF PLASMODESMATA
17 QuantificationofCell-to-CellConnectivityUsingParticle
Bombardment.......................................................... 263
EsteeE.Tee,SebastianSamwald,andChristineFaulkner
18 InvestigatingPlasmodesmataFunctioninArabidopsisThaliana
UsingaLow-PressureBombardmentSystemandGFPMovementAssay ...... 273
JessicaC.FernandezandTessaM.Burch-Smith
19 QuantifyingPlasmodesmatalTransportwithanImprovedGFPMovement
Assay.................................................................. 285
WilsonHornerandJacobO.Brunkard
20 AnArabidopsisCallusGraftingMethodtoTestCell-to-CellMobility
ofProteins............................................................. 299
FrankMachin,Yag˘murHasbiog˘lu,andFriedrichKragler
21 QuantificationofPlasmodesmataPermeabilityinArabidopsisLeaves
byTracingtheMovementofGFP ........................................ 313
MinDiaoandShanjinHuang
22 TrackingIntercellularMovementofFluorescentProteinsinBryophytes....... 321
TakumiTomoi,YoanCoudert,andTomomichiFujita
23 VirusGenome-BasedReporter forAnalyzingViralMovementProteins
andPlasmodesmataPermeability.......................................... 333
EkaterinaA.Lazareva, AnastasiaK.Atabekova,AlexanderA.Lezzhov,
SergeyY.Morozov,ManfredHeinlein,andAndreyG.Solovyev
24 AnalysisoftheDistributionofSymplasmicTracersDuringZygotic
andSomaticEmbryogenesis.............................................. 351
JustynaWr(cid:1)obel-Marek,KamilaGodel-Je˛drychowska,
andEwaKurczyn´ska
Contents ix
25 QuantifyingIntercellularMovementandProteinStoichiometry
forComputationalModeling............................................. 367
LisaVandenBroeck,MariahGobble,andRosangelaSozzani
26 SpatiotemporalSpecificBlockingofPlasmodesmatabyCallose
Induction.............................................................. 383
DaweiYan
27 AForwardGeneticApproachtoIdentifyPlasmodesmalTrafficking
RegulatorsBasedonTrichomeRescue .................................... 393
MunenoriKitagawaandDavidJackson
PART V OTHER APPROACHES CONTRIBUTING TO PLASMODESMATA
RESEARCH
28 InVivoVisualizationofMobilemRNAParticlesinPlantsUsingBglG........ 411
EduardoJ.Pen˜aandManfredHeinlein
29 Multi-AngleInVivoImagingoftheArabidopsisthalianaShoot
ApicalMeristem(SAM).................................................. 427
MichaelFuchsandJanU.Lohmann
30 MoreInsightsfromUltrastructuralandFunctionalPlasmodesmata
DataUsingPDinsight................................................... 443
EvaE.Deinum
31 MeasuringIntercellularInterfaceAreainPlantTissuesUsingQuantitative
3DImageAnalysis...................................................... 457
GwendolynV.Davis,RichardS.Smith,andGeorgeW.Bassel
Index ...................................................................... 465
Contributors
SAMAMSBURY • SchoolofBiosciences,TheUniversityofSheffield,Sheffield,UK
ANASTASIA K.ATABEKOVA • DepartmentofVirology,BiologicalFaculty,MoscowState
University,Moscow,Russia;A.N.BelozerskyInstituteofPhysico-ChemicalBiology,Moscow
StateUniversity,Moscow,Russia
GEORGEW.BASSEL • SchoolofLifeSciences,TheUniversityofWarwick,Coventry,UK
EMMANUELLEM.F.BAYER • LaboratoiredeBioge`neseMembranaire,UMR5200,CNRS,
Universite´deBordeaux,Villenaved’OrnonCedex,France
ILYABELEVICH • HelsinkiInstituteofLifeScience/InstituteofBiotechnology,Universityof
Helsinki,Helsinki,Finland
YOSELINBENITEZ-ALFONSO • CentreforPlantScience,SchoolofBiology,UniversityofLeeds,
Leeds,UK
PATRICKBLU¨MKE • InstituteforDevelopmentalGenetics,HeinrichHeineUniversity,
Du¨sseldorf,Germany
STANLEYW.BOTCHWAY • CentralLaserFacility,ScienceandTechnologyFacilitiesCouncil
(STFC),RutherfordAppletonLaboratory,ResearchComplexatHarwell,Didcot,UK
LYSIANEBROCARD • BordeauxImagingCentre,PlantImagingPlatform,UMS3420,
INRA-CNRS-INSERM-UniversityofBordeaux,Villenaved’Ornon,France
JACOBO.BRUNKARD • LaboratoryofGenetics,UniversityofWisconsin-Madison,Madison,
WI,USA;DepartmentofPlantandMicrobialBiology,UniversityofCaliforniaat
Berkeley,Berkeley,CA,USA;PlantGeneExpressionCenter,U.S.Departmentof
Agriculture,AgriculturalResearchService,Albany,CA,USA
TESSAM.BURCH-SMITH • DepartmentofBiochemistry&CellularandMolecularBiology,
UniversityofTennessee,Knoxville,TN,USA;DonaldDanforthPlantScienceCenter,
SaintLouis,MO,USA
AJEETCHAUDHARY • PlantDevelopmentalBiology,TUMSchoolofLifeSciences,Technical
UniversityofMunich,Freising,Germany;DepartmentofPlantBiology,Carnegie
InstitutionforScience,Stanford,CA,USA
STE´PHANECLAVEROL • PlateformeProteome,Universite´deBordeaux,Bordeaux,France
YOANCOUDERT • LaboratoireReproductionetDe´veloppementdesPlantes,ENSdeLyon,
Lyon,France
FLORENCER.DANILA • ResearchSchoolofBiology,TheAustralianNationalUniversity,
Acton,ACT,Australia
GWENDOLYNV.DAVIS • SchoolofLifeSciences,TheUniversityofWarwick,Coventry,UK
EVAE.DEINUM • WageningenUniversity,Wageningen,TheNetherlands
MINDIAO • iHumanInstitute,ShanghaiTechUniversity,Shanghai,China
JOHNR.DUNLAP • TheJointInstituteforAdvancedMaterials,UniversityofTennessee,
Knoxville,TN,USA
CHRISTINEFAULKNER • CropGenetics,JohnInnesCentre,NorwichResearchPark,Norwich,
UK
JESSICAC.FERNANDEZ • DepartmentofBiochemistry&CellularandMolecularBiology,
UniversityofTennessee,Knoxville,TN,USA;DepartmentofBotany,Universityof
Wisconsin,Madison,WI,USA
xi