The Unfolded Protein Response: Methods and Protocols

326 Pages·2022·10.046 MB·English

by  Roberto Pérez-Torrado

Methods in
Molecular Biology 2378
Roberto Pérez-Torrado Editor
The Unfolded
Protein
Response
Methods and Protocols
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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The Unfolded Protein Response
Methods and Protocols
Edited by
Roberto Pérez-Torrado
Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Paterna, Spain
Editor
RobertoPe´rez-Torrado
InstitutodeAgroqu´ımicayTecnolog´ıa
deAlimentos
CSIC
Paterna,Spain
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-1731-1 ISBN978-1-0716-1732-8 (eBook)
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Preface: Molecular Methodologies to Understand the UPR
Pathway
The Unfolded Protein Pathway was first discovered by Shiu et al. [1] in 1971 when the
authors described a rapid increase in the levels of two proteins in the lumen of the
endoplasmic reticulum after glucose starvation in mammalian cells. In the last decades,
many advances have attracted the attention of researchers of life sciences due to the broad
implications of the UPR pathway machinery in the proper functioning of the cells. It
responds to a myriad of signals and is implicated in a number of human diseases as
neurodegenerative or metabolic dysfunctions. Thus, the study of this pathway and the
outcomes of its activation and external modulators will gain a notorious relevance in the
nextyears.ThisvolumeofMethodsinMolecularBiologyseriesisdividedintosixsectionsto
covermostoftheexperimentalapproachesinvolvedinthestudyoftheUPRpathwayandto
provide the reader with a comprehensive and practical laboratory manual, a valuable
resource to expand research on the field. We bring together prominent scientist in the
field to describe key methods and approaches used in the study of the UPR pathway and
itscomplexcellularimplications.
Paterna,Spain RobertoPe´rez-Torrado
References
1. Shiu RP, Pouyssegur J, Pastan I (1971) Glucose depletion accounts for the induction of two
transformation-sensitivemembraneproteinsinRoussarcomavirus–transformedchickembryofibro-
blasts.ProcNatlAcadSciUSA74:3840–3844.
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I DETERMINATION OF UNFOLDED PROTEIN LEVELS
1 MeasuringCysteineExposureinUnfoldedProteinswithTetraphenylethene
MaleimideanditsAnalogs ............................................... 3
ShouxiangZhangandYuningHong
2 Fluorescence-BasedBiosensorsfor theDetectionoftheUnfolded
ProteinResponse ....................................................... 19
HeinrichKroukamp,KaiPeng,IanT.Paulsen,andRiaandenHaan
3 IndirectMethodsToMeasureUnfoldedProteinsInLivingCells
UsingFluorescentProteins............................................... 31
ElisabetNavarro-TapiaandRobertoPe´rez-Torrado
4 APlatform TechnologyforMonitoringtheUnfoldedProteinResponse....... 45
BhagyashreeBachhav,CarlosA.OrigelMarmolejo,YafetArefeayne,
andLauraSegatori
5 TheUseofFluorescentProteinFusionstoMonitor theUnfolded
ProteinResponseandProteinFoldase-SubstrateInteractions
inPlantProtoplasts ..................................................... 69
RinaCarrillo,ElizabethFeldeverd,andDavidA.Christopher
PART II METHODS TO STUDY UPR SIGNAL TRANSMISSION
6 High-ThroughputAnalysisofProteinTurnover withTandem
FluorescentProteinTimers............................................... 85
JiaJunFung,KarlaBl¨ocher-Jua´rez,andAntonKhmelinskii
7 DetectionofHAC1mRNASplicingbyRT-PCR
inSaccharomycescerevisiae................................................ 101
JagadeeshKumarUppalaandMadhusudanDey
PART III ANALYSING THE OUTCOMES OF THE UPR PATHWAYACTIVATION
8 DetectingtheNon-conventionalmRNASplicingandTranslationalActivation
ofHAC1inBuddingYeast............................................... 113
WeihanLiandRobertH.Singer
9 DeterminationoftheStabilityandIntracellular(Intra-Nuclear)Targeting
andRecruitmentofPre-HAC1mRNAintheSaccharomycescerevisiae
DuringtheActivationofUPR............................................ 121
SunirmalPairaandBiswadipDas
10 AssaystoStudyIRE1ActivationandSignaling ............................. 141
PalomaMoraga,RaulAravena,HeryUrra,andClaudioHetz
vii
viii Contents
11 AnalysisofXBP1ContributiontoHyperosmolarity-Induced
LipidSynthesis ......................................................... 169
CeciliaI.Casali,LeandroParra,LucianaC.Erjavec,
andMarı´adelCarmenFerna´ndezTome
12 IntegratinganERStressReporter forMonitoringGenome-Wide
UPR-ERinBuddingYeast............................................... 189
ShuvadeepMaity,AsmitaGhosh,andKausikChakraborty
PART IV UPR STUDIES IN MAMMALIAN MODELS
13 AnalyzeMouseKnockoutModelsofUPRPathwayElements................ 205
ChaoZheng,ChengWang,QiangJie,andLiuYang
14 InVitroStimulationofIRE1α/XBP1-DeficientBCellswithLPS ............ 221
HuabinZhu,ChenJiang,RandalJ.Kaufman,HonglinLi,
andNagendraSingh
15 DetectionofPERKSignalingintheCentralNervousSystem ................ 233
ZhixinLei,SarrabethStone,andWenshengLin
PART V UPR IN ALTERNATIVE MODELS
16 MethodstoStudytheMitochondrialUnfoldedProteinResponse(UPRmt)
inCaenorhabditiselegans ................................................ 249
SimonHaeusslerandBarbaraConradt
17 DrosophilaUnfoldedProteinResponse(UPR)Assays
InVitroandInVivo .................................................... 261
HidetakaKatow,DeepikaVasudevan,andHyungDonRyoo
18 ProteinPreparationforProteomicAnalysisoftheUnfolded
ProteinResponseinArabidopsisthaliana.................................. 279
YuntingPuandFedericaBrandizzi
PART VI UPR AND DISEASE
19 Structure-BasedDrugDiscoveryofIRE1Modulators....................... 293
DianaPelizzariRaymundo,LeifA.Eriksson,EricChevet,
andXavierGuillory
20 HTSIdentificationofActivatorsandInhibitorsofEndoplasmicReticulum(ER)
StressandtheUnfoldedProteinResponse(UPR) .......................... 317
MehrnooshGhafouri,ChesterB.Gauss,andAndrewM.Fribley
Index ...................................................................... 329
Contributors
RAULARAVENA • FacultyofMedicine,BiomedicalNeuroscienceInstitute(BNI),University
ofChile,Santiago,Chile;Center forGeroscience,BrainHealthandMetabolism(GERO),
Santiago,Chile;ProgramofCellularandMolecularBiology,InstituteofBiomedical
Sciences(ICBM),UniversityofChile,Santiago,Chile
YAFETAREFEAYNE • DepartmentofBioengineering,RiceUniversity,Houston,TX,USA
BHAGYASHREEBACHHAV • DepartmentofChemicalandBiomolecularEngineering,Rice
University,Houston,TX,USA
KARLABLO¨CHER-JUA´REZ • InstituteofMolecularBiology(IMB),Mainz,Germany
FEDERICA BRANDIZZI • MSU-DOEPlantResearchLabandPlantBiologyDepartment,
MichiganStateUniversity,EastLansing,MI,USA
RINACARRILLO • DepartmentofMolecularBiosciences&Bioengineering,Universityof
Hawaii,Honolulu,HI,USA
CECILIAI.CASALI • Ca´tedradeBiologı´aCelular yMolecular,DepartamentodeCiencias
Biol(cid:1)ogicas,FacultaddeFarmaciayBioquı´mica,UniversidaddeBuenosAires,Buenos
Aires,Argentina;InstitutodeQuı´micayFisicoquı´micaBiol(cid:1)ogicasProf.Dr.AlejandroC.
Paladini(IQUIFIB),ConsejoNacionaldeInvestigacionesCientı´ficasyTe´cnicas
(CONICET),BuenosAires,Argentina
KAUSIKCHAKRABORTY • CSIR-InstituteofGenomicsandIntegrativeBiology,NewDelhi,
India
ERICCHEVET • INSERMU1242,Universite´deRennes,Rennes,France;CentredeLutte
contreleCancerEuge`neMarquis,Rennes,France
DAVIDA.CHRISTOPHER • DepartmentofMolecularBiosciences&Bioengineering,University
ofHawaii,Honolulu,HI,USA
BARBARACONRADT • ResearchdepartmentofCellandDevelopmentalBiology,Divisionof
Biosciences,UniversityCollegeLondon,London,UK
BISWADIPDAS • DepartmentofLifeScienceandBiotechnology,JadavpurUniversity,
Kolkata,India
MARI´ADEL CARMEN FERNA´NDEZTOME • Ca´tedradeBiologı´aCelular yMolecular,
DepartamentodeCienciasBiol(cid:1)ogicas,FacultaddeFarmaciayBioquı´mica,Universidad
deBuenosAires,BuenosAires,Argentina;InstitutodeQuı´micayFisicoquı´micaBiol(cid:1)ogicas
Prof.Dr.AlejandroC.Paladini(IQUIFIB),ConsejoNacionaldeInvestigaciones
Cientı´ficasyTe´cnicas(CONICET),BuenosAires,Argentina
RIAAN DENHAAN • DepartmentofBiotechnology,UniversityoftheWesternCape,Bellville,
SouthAfrica
MADHUSUDANDEY • DepartmentofBiologicalSciences,UniversityofWisconsin-Milwaukee,
Milwaukee,WI,USA
LEIF A.ERIKSSON • DepartmentofChemistryandMolecularBiology,Universityof
Gothenburg,Go¨teborg,Sweden
LUCIANAC.ERJAVEC • Ca´tedradeBiologı´aCelular yMolecular,DepartamentodeCiencias
Biol(cid:1)ogicas,FacultaddeFarmaciayBioquı´mica,UniversidaddeBuenosAires,Buenos
Aires,Argentina;InstitutodeQuı´micayFisicoquı´micaBiol(cid:1)ogicasProf.Dr.AlejandroC.
Paladini(IQUIFIB),ConsejoNacionaldeInvestigacionesCientı´ficasyTe´cnicas
(CONICET),BuenosAires,Argentina
ix
x Contributors
ELIZABETHFELDEVERD • DepartmentofMolecularBiosciences&Bioengineering,University
ofHawaii,Honolulu,HI,USA
ANDREWM.FRIBLEY • CarmanandAnnAdamsDepartmentofPediatrics,WayneState
UniversitySchoolofMedicine,Detroit,MI,USA;DepartmentofOtolaryngology—Head
andNeckSurgery,WayneStateUniversitySchoolofMedicine,Detroit,MI,USA;
MolecularTherapeuticsProgram,BarbaraAnnKarmanosCancerInstitute,Detroit,
MI,USA
JIAJUNFUNG • InstituteofMolecularBiology(IMB),Mainz,Germany
CHESTERB.GAUSS • CarmanandAnnAdamsDepartmentofPediatrics,WayneState
UniversitySchoolofMedicine,Detroit,MI,USA
MEHRNOOSHGHAFOURI • CarmanandAnnAdamsDepartmentofPediatrics,WayneState
UniversitySchoolofMedicine,Detroit,MI,USA
ASMITAGHOSH • DepartmentofNeurosciences,CentreHospitalierdel’Universitede
Montreal(CHUM)ResearchCenter,Montreal,QC,Canada;CSIR-InstituteofGenomics
andIntegrativeBiology,NewDelhi,India
XAVIERGUILLORY • INSERMU1242,Universite´deRennes,Rennes,France;CentredeLutte
contreleCancerEuge`neMarquis,Rennes,France;UnivRennes,CNRSISCR(Institut
desScienceChimiquesdeRennes)—UMR6226,Rennes,France
SIMONHAEUSSLER • FacultyofBiology,Ludwig-Maximilians-UniversityMunich,Planegg-
Martinsried,Germany
CLAUDIOHETZ • FacultyofMedicine,BiomedicalNeuroscienceInstitute(BNI),University
ofChile,Santiago,Chile;Center forGeroscience,BrainHealthandMetabolism(GERO),
Santiago,Chile;ProgramofCellularandMolecularBiology,InstituteofBiomedical
Sciences(ICBM),UniversityofChile,Santiago,Chile;TheBuckInstituteforResearchin
Aging,Novato,CA,USA
YUNINGHONG • DepartmentofChemistryandPhysics,LaTrobeInstituteforMolecular
Science,LaTrobeUniversity,Melbourne,VIC,Australia
CHENJIANG • DepartmentofBiochemistryandMolecularBiology,GeorgiaCancerCenter,
AugustaUniversity,August,GA,USA
QIANGJIE • DepartmentofOrthopedicSurgery,HongHuiHospital,Xi’anJiaotong
University,CollegeofMedicine,Xi’an,China
HIDETAKA KATOW • DepartmentofCellBiology,NewYorkUniversityGrossmanSchoolof
Medicine,NewYork,NY,USA
RANDALJ.KAUFMAN • DegenerativeDiseasesProgram,SanfordBurnhamPrebys,Medical
DiscoveryInstitute,LaJolla,CA,USA
ANTON KHMELINSKII • InstituteofMolecularBiology(IMB),Mainz,Germany
HEINRICH KROUKAMP • DepartmentofMolecularSciences,ARCCentreofExcellencein
SyntheticBiology,MacquarieUniversity,Sydney,NSW,Australia;BiomolecularDiscovery
andDesignResearchCentre,MacquarieUniversity,Sydney,NSW,Australia
ZHIXINLEI • DepartmentofNeuroscience,UniversityofMinnesota,Minneapolis,MN,USA;
InstituteforTranslationalNeuroscience,UniversityofMinnesota,Minneapolis,MN,USA
HONGLINLI • DepartmentofBiochemistryandMolecularBiology,GeorgiaCancerCenter,
AugustaUniversity,August,GA,USA
WEIHANLI • DepartmentofAnatomyandStructuralBiology,AlbertEinsteinCollegeof
Medicine,Bronx,NY,USA
WENSHENGLIN • DepartmentofNeuroscience,UniversityofMinnesota,Minneapolis,MN,
USA;InstituteforTranslationalNeuroscience,UniversityofMinnesota,Minneapolis,
MN,USA