Intracellular Lipid Transport: Methods and Protocols

347 Pages·2019·8.298 MB·English

by  Guillaume Drin

Methods in
Molecular Biology 1949
Guillaume Drin Editor
Intracellular
Lipid
Transport
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences,
University ofHertfordshire,
Hatfield, Hertfordshire AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Intracellular Lipid Transport
Methods and Protocols
Edited by
Guillaume Drin
Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur and CNRS, Valbonne, France
Editor
GuillaumeDrin
InstitutdePharmacologieMole´culaireetCellulaire
Universite´Coˆted’AzurandCNRS
Valbonne,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9135-8 ISBN978-1-4939-9136-5 (eBook)
https://doi.org/10.1007/978-1-4939-9136-5
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Preface
The boundaries and complex architecture of cells rely on membranes that result from the
assembly of many lipids, along with proteins. Lipid chemistry is highly diverse with
thousands of lipid species identified to date. Inside prokaryotic and eukaryotic cells, lipid
species are not randomly distributed between membranes, quite the contrary. In actuality,
membranesareendowedwithprecisephysicochemicalfeaturesandselectivelyhostparticu-
larlipidswithsignalingroles.Forinstance,itiswelldescribedthat,ineukaryoticcells,each
organellemembranehasitsownmolecular identity,whichisessentialfor manyproteinsto
function properly and support key functions. At any time, underlying mechanisms adjust
and maintain the lipid composition of membranes in the face of permanent processes that
locallymodifythelipidcomposition,suchastheuseofcertainlipidsbysignalingpathways,
or the mixing of lipids, as in eukaryotic cells, by vesicular trafficking that causes massive
membrane exchange. Those mechanisms are the metabolic pathways that ensure lipid
synthesis, interconversion, and degradation as well as processes that ensure lipid transport
within and between membranes. Yet, while metabolic processes are well defined, relatively
littleisknownaboutintracellularlipidtransport.
A likely reason is that intracellular lipid transport routes are by nature quite elusive.
Besides, the mechanisms whereby lipid transfer proteins (LTPs) and scramblases/flippases
move lipids between and in organelle membranes, respectively, remain still mysterious.
Better deciphering of these transport processes is crucial to apprehend how a cell ensures
some of its key functions. For instance, recent studies have unveiled that the signaling
competence of cells relies on fast lipid exchange between the endoplasmic reticulum and
the plasma membrane. Another key motivation to explore how lipid transporters work
relates to the fact that they can be at the origin or involved in some cellular dysfunctions,
resulting in acute syndromes. An archetypical example is the Niemann-Pick type C disease
whicharisesfromadefectofaLTPcalledNPC1,causinganaberrantaccumulationofsterol
in lysosomes. We also know, for instance, that the overactivity of the sterol-transporter
STARD3 is a marker of poor prognosis in breast cancer or that lipid transport routes are
hijacked by human viruses to remodel organelles into replication sites. Along with this,
proof-of-conceptstudiesshowedthatLTPsarepotentialpharmacologicaltargets.
In parallel with a growing interest in membrane contact sites, which correspond to
singular regions where two organelles are in close apposition, and the discovery of new
classes of lipid transporters and major advances in solving their tridimensional structure, a
great ingenuity is currently deployed to understand at different scale how lipids are accu-
rately displaced between organelles, across long-distance or in membrane contact sites, or
insidecellularmembranes.Thegoalofthisbookistoprovidetechnicalapproachestotackle
various questions related to intracellular lipid transport. It encompasses chapters from
leading experts in this realm who outline step-by-step protocols they developed during
recentyears.
Severalchapters,whichconstitutethefirstpartofthisvolume,exposemethodologiesto
measure the movement of varied lipid species (glycerophospholipid, sphingolipids, sterol,
etc.)betweenorinorganellemembranes,insideeukaryoticcells,includingplantcells,orin
bacteria.Differentapproachesaredescribed,amongwhicharecellimagingandbiolumines-
cence resonance energy transfer (BRET), relying on the use of fluorescent lipids or
v
vi Preface
genetically encoded lipid probes, as well as organelle isolation strategies coupled to lipid
analysis. Of a great diversity, these methodologies all offer researchers the ability to follow
particularlipidtype(s)outofmanyothersinthecomplexenvironmentofacell,notablyin
membranecontactsites,withthehighestaccuracyandthebestpossibletemporalresolution.
The second part of the book gathers in vitro or in silico approaches aiming to define,
more from biochemical and structural standpoints, how LTPs or flippases/scramblases
precisely function. Protocols that are presented allow for answering questions like, “What
sort of lipids are recognized by my favorite LTP? At which speed is my protein capable of
moving lipids between two distinct organelles or, in the case of a flippase/scramblase, to
displace lipids transversally between the two sides of a membrane?” These approaches are
useful to define what the affinity and selectivity of a transporter for lipid ligand(s) are.
Moreover, based on the use of artificial membranes called liposomes, these protocols offer
a unique way to precisely establish the velocity of transporters while indicating how some
membrane parameters (surface charge, fluidity, etc.) or cofactors (ions) influence their
activity. One chapter describes protocols to measure how a LTP, working at contact sites,
tetherstwomembranesandtransferslipidsinbetween.Onechapterdescribesthemakingof
new lipids that can be useful to improve in vitro transfer assays. Lastly, a chapter presents
how to perform reliable molecular dynamic simulations to describe what likely happens at
theatomiclevelwhenaLTPdocksontoamembranesurface,astepthatstillremainsquite
enigmatic.
Valbonne,France GuillaumeDrin
Contents
Preface ..................................................................... v
Contributors................................................................. xi
1 AnalysisofPhosphatidylinositolTransferatER-PMJunctions
inReceptor-StimulatedLiveCells......................................... 1
Chi-LunChangandJenLiou
2 MonitoringNon-vesicularTransportofPhosphatidylserine
andPhosphatidylinositol4-PhosphateinIntactCellsbyBRETAnalysis ....... 13
MiraSohn,DanielJ.Toth,andTamasBalla
3 DevelopmentofNonspecificBRET-BasedBiosensors
toMonitorPlasmaMembraneInositolLipidsinLivingCells................. 23
J(cid:1)ozsefT.T(cid:1)oth,Gergo˝Gulya´s,La´szl(cid:1)o Hunyady,andPe´terVa´rnai
4 FollowingAnterogradeTransportofPhosphatidylserine
inYeastinRealTime.................................................... 35
JuanMartı´nD’Ambrosio,Ve´roniqueAlbane`se,andAlenkaCˇopicˇ
5 ImagingLipidMetabolismattheGolgiComplex........................... 47
SerenaCapassoandGiovanniD’Angelo
6 AdvancedInVitroAssaySystemtoMeasurePhosphatidylserine
andPhosphatidylethanolamineTransportatER/MitochondriaInterface ...... 57
YasushiTamura,RiekoKojima,andToshiyaEndo
7 MeasurementofLipidTransportinMitochondriabytheMTLComplex...... 69
JulietteJouhet,Vale´rieGros,andMorganeMichaud
8 Bi-andTrifunctionalLipidsforVisualizationofSphingolipid
DynamicswithintheCell ................................................ 95
DorisH¨oglinger
9 IndirectLipidTransferProteinActivityMeasurementsUsing
QuantificationofGlycosphingolipidProduction............................ 105
AndersP.E.Backman,JosefinHalin,MattiA.Kjellberg,
andPeterMattjus
10 MeasurementofIntracellularSterolTransportinYeast...................... 115
NehaChauhan,JulianA.Jentsch,andAnantK.Menon
11 IntracellularandPlasmaMembraneCholesterolLabeling
andQuantificationUsingFilipinandGFP-D4 ............................. 137
Le´aP.Wilhelm,LaetitiaVoilquin,ToshihideKobayashi,
CatherineTomasetto,andFabienAlpy
12 MonitoringandModulatingIntracellularCholesterol
TraffickingUsingALOD4,aCholesterol-BindingProtein................... 153
Shreya Endapally,RodneyE.Infante,andArunRadhakrishnan
13 MeasurementofLysophospholipidTransportAcrosstheMembrane
UsingEscherichiacoliSpheroplasts........................................ 165
YibinLin,LeiZheng,andMikhailBogdanov
vii
viii Contents
14 PreparationofProteoliposomeswithPurifiedTMEM16
ProteinforAccurateMeasuresofLipidScramblaseActivity .................. 181
JanineDeniseBrunnerandStephanSchenck
15 InVitroAssaystoMeasuretheMembraneTetheringandLipid
TransportActivitiesoftheExtendedSynaptotagmins ....................... 201
XinBianandPietroDeCamilli
16 DeterminingtheLipid-BindingSpecificityofSMPDomains:
AnERMESSubunitasaCaseStudy ...................................... 213
AndrewP.AhYoungandPascalF.Egea
17 InVitroMeasurementofSphingolipidIntermembraneTransport
IllustratedbyGLTPSuperfamilyMembers................................. 237
RoopaKenoth,RhoderickE.Brown,andRaviKanthKamlekar
18 PurificationandCharacterizationofHumanNiemann–PickC1Protein....... 257
XinGongandHongwuQian
19 InVitroStrategytoMeasureSterol/Phosphatidylinositol-4-Phosphate
ExchangeBetweenMembranes........................................... 269
Nicolas-Fre´de´ricLippandGuillaumeDrin
20 DeterminationofLigandBindingAffinityandSpecificity
ofPurifiedSTARTDomainsbyThermalShiftAssaysUsing
CircularDichroism...................................................... 293
DannyLe´tourneau,Jean-GuyLeHoux,andPierreLavigne
21 SynthesisofFluorescentMembrane-SpanningLipidsforStudies
ofLipidTransferandMembraneFusion................................... 307
Gu¨nterSchwarzmann
22 SettingUpAll-AtomMolecularDynamicsSimulations
toStudytheInteractionsofPeripheralMembraneProteins
withModelLipidBilayers................................................ 325
VivianaMonje-Galvan,LinneaWarburton,andJefferyB.Klauda
Index ...................................................................... 341
Contributors
ANDREWP.AHYOUNG (cid:1) DepartmentofBiologicalChemistry,DavidGeffenSchoolof
Medicine,UniversityofCalifornia,LosAngeles,CA,USA;DepartmentofEarlyDiscovery
Biochemistry,GenentechInc.,SouthSanFrancisco,CA,USA
VE´RONIQUEALBANE`SE (cid:1) InstitutJacquesMonod,CNRS,Universite´ParisDiderot,Sorbonne
ParisCite´,Paris,France
FABIENALPY (cid:1) InstitutdeGe´ne´tiqueetdeBiologieMole´culaireetCellulaire(IGBMC),
InstitutNationaldelaSante´etdelaRechercheMe´dicale(INSERM),U1258,Centre
NationaldelaRechercheScientifique(CNRS),UMR7104andUniversite´deStrasbourg,
Illkirch,France
ANDERSP.E.BACKMAN (cid:1) FacultyofScienceandEngineering,Biochemistry,A˚boAkademi
University,Turku,Finland
TAMASBALLA (cid:1) SectiononMolecularSignalTransduction,EuniceKennedyShriverNational
InstituteofChildHealthandHumanDevelopment,NationalInstitutesofHealth,
Bethesda,MD,USA
XINBIAN (cid:1) DepartmentofNeuroscienceandCellBiology,HowardHughesMedicalInstitute,
PrograminCellularNeuroscience,Neurodegeneration,andRepair,andKavliInstitute
forNeuroscience,YaleUniversitySchoolofMedicine,NewHaven,CT,USA
MIKHAILBOGDANOV (cid:1) DepartmentofBiochemistryandMolecularBiology,Universityof
TexasHealthScienceCenteratHoustonMcGovernMedicalSchool,Houston,TX,USA;
DepartmentofBiochemistryandBiotechnology,InstituteofFundamentalMedicineand
Biology,KazanFederalUniversity,Kazan,RussianFederation
RHODERICKE.BROWN (cid:1) TheHormelInstitute,UniversityofMinnesota,Austin,MN,USA
JANINE DENISEBRUNNER (cid:1) LaboratoryofBiomolecularResearch,DivisionofBiologyand
Chemistry,PaulScherrerInstitute,Villigen,Switzerland
SERENACAPASSO (cid:1) InstituteofProteinBiochemistry,NationalCouncilResearch,Naples,
Italy;IRBM,Rome,Italy
CHI-LUN CHANG (cid:1) JaneliaResearchCampus,HowardHughesMedicalInstitute,Ashburn,
VA,USA
NEHACHAUHAN (cid:1) DepartmentofBiochemistry,WeillCornellMedicalCollege,NewYork,
NY,USA
ALENKACˇOPICˇ (cid:1) InstitutJacquesMonod,CNRS,Universite´ParisDiderot,SorbonneParis
Cite´,Paris,France
JUANMARTI´ND’AMBROSIO (cid:1) InstitutJacquesMonod,CNRS,Universite´ParisDiderot,
SorbonneParisCite´,Paris,France
GIOVANNID’ANGELO (cid:1) InstituteofProteinBiochemistry,NationalCouncilResearch,Naples,
Italy
PIETRODECAMILLI (cid:1) DepartmentofNeuroscienceandCellBiology,HowardHughes
MedicalInstitute,PrograminCellularNeuroscience,Neurodegeneration,andRepair,
andKavliInstituteforNeuroscience,YaleUniversitySchoolofMedicine,NewHaven,CT,
USA
GUILLAUMEDRIN (cid:1) Universite´Coˆted’Azur,CNRS,InstitutdePharmacologieMole´culaireet
Cellulaire,Valbonne,France
ix
x Contributors
PASCALF.EGEA (cid:1) DepartmentofBiologicalChemistry,DavidGeffenSchoolofMedicine,
UniversityofCalifornia,LosAngeles,CA,USA;TheMolecularBiologyInstitute,
UniversityofCalifornia,LosAngeles,LosAngeles,CA,USA
SHREYAENDAPALLY (cid:1) DepartmentofMolecularGenetics,UniversityofTexasSouthwestern
MedicalCenter,Dallas,TX,USA
TOSHIYAENDO (cid:1) FacultyofLifeSciences,KyotoSangyoUniversity,Kyoto,Japan
XINGONG (cid:1) DepartmentofBiology,SouthernUniversityofScienceandTechnology,Shenzhen,
Guangdong,China;DepartmentofMolecularBiology,PrincetonUniversity,Princeton,
NJ,USA
VALE´RIEGROS (cid:1) LaboratoiredePhysiologieCellulaireetVe´ge´tale,UMR5168CNRS-CEA-
INRA-Universite´GrenobleAlpes,Grenoble,France
GERGO˝ GULYA´S (cid:1) FacultyofMedicine,DepartmentofPhysiology,SemmelweisUniversity,
Budapest,Hungary
JOSEFINHALIN (cid:1) FacultyofScienceandEngineering,Biochemistry,A˚boAkademiUniversity,
Turku,Finland
DORISHO¨GLINGER (cid:1) HeidelbergUniversityBiochemistryCenter,Heidelberg,Germany
LA´SZLO´ HUNYADY (cid:1) FacultyofMedicine,DepartmentofPhysiology,SemmelweisUniversity,
Budapest,Hungary;MTA-SELaboratoryofMolecularPhysiology,Budapest,Hungary
RODNEYE.INFANTE (cid:1) DepartmentofMolecularGeneticsandInternalMedicine,andCenter
forHumanNutrition,UniversityofTexasSouthwesternMedicalCenter,Dallas,TX,USA
JULIANA.JENTSCH (cid:1) DepartmentofBiochemistry,WeillCornellMedicalCollege,NewYork,
NY,USA;InstituteforPathophysiology,WestGermanHeartandVascularCentre,
UniversityHospitalEssen,Essen,Germany
JULIETTEJOUHET (cid:1) LaboratoiredePhysiologieCellulaireetVe´ge´tale,UMR5168CNRS-
CEA-INRA-Universite´GrenobleAlpes,Grenoble,France
RAVIKANTHKAMLEKAR (cid:1) DepartmentofChemistry,SchoolofAdvancedSciences,VIT,Vellore,
TamilNadu,India
ROOPAKENOTH (cid:1) DepartmentofChemistry,SchoolofAdvancedSciences,VIT,Vellore,Tamil
Nadu,India
MATTIA.KJELLBERG (cid:1) FacultyofScienceandEngineering,Biochemistry,A˚boAkademi
University,Turku,Finland
JEFFERYB.KLAUDA (cid:1) DepartmentofChemicalandBiomolecularEngineering,Universityof
Maryland,CollegePark,MD,USA;BiophysicsProgram,UniversityofMaryland,College
Park,MD,USA
TOSHIHIDEKOBAYASHI (cid:1) Universite´deStrasbourgandLaboratoryofBioimagingand
Pathologies,CentreNationaldelaRechercheScientifique(CNRS),UMR7021,Illkirch,
France
RIEKOKOJIMA (cid:1) FacultyofScience,YamagataUniversity,Yamagata,Japan
PIERRELAVIGNE (cid:1) Faculte´deMe´decineetdesSciencesdelaSante´,De´partementdeBiochimie,
Universite´deSherbrooke,Sherbrooke,QC,Canada
JEAN-GUYLEHOUX (cid:1) Faculte´deMe´decineetdesSciencesdelaSante´,De´partementde
Biochimie,Universite´deSherbrooke,Sherbrooke,QC,Canada
DANNYLE´TOURNEAU (cid:1) Faculte´deMe´decineetdesSciencesdelaSante´,De´partementde
Biochimie,Universite´deSherbrooke,Sherbrooke,QC,Canada
YIBINLIN (cid:1) DivisionofInfectiousDiseases,DepartmentofPediatrics,Center for
AntimicrobialResistanceandMicrobialGenomics,UniversityofTexasHealthScience
CenteratHoustonMcGovern MedicalSchool,Houston,TX,USA
JENLIOU (cid:1) DepartmentofPhysiology,UTSouthwesternMedicalCenter,Dallas,TX,USA