Intermediate filament associated proteins

563 Pages·2016·51.535 MB·English

by  Sonnenberg, Arnoud, Wilson, Katherine L

METHODS IN ENZYMOLOGY
Editors-in-Chief
ANNA MARIE PYLE
Departments of Molecular, Cellular and Developmental
Biology and Department of Chemistry Investigator
Howard Hughes Medical Institute
Yale University
DAVID W. CHRISTIANSON
Roy and Diana Vagelos Laboratories
Department of Chemistry
University of Pennsylvania
Philadelphia, PA
Founding Editors
SIDNEY P. COLOWICK and NATHAN O. KAPLAN
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CONTRIBUTORS
NoeliaAlonso-Garc´ıa
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
RuthellenH.Anderson
SanfordChildren’sHealthResearchCenter,SanfordResearch,SiouxFalls,SouthDakota,
USA
ChristopherArnette
DepartmentofPathology,NorthwesternUniversityFeinbergSchoolofMedicine,Chicago,
Illinois,USA
PeterAskjaer
AndalusianCenterforDevelopmentalBiology,CSIC-JuntadeAndalucia-Universidad
PablodeOlavide,CarreteradeUtrera,Seville,Spain
PetrosBatsios
InstituteforBiochemistryandBiology,DepartmentofCellBiology,UniversityofPotsdam,
Potsdam,Germany
NadjaBegre´
DepartmentofClinicalResearch,UniversityofBern,andDepartmentofDermatology,
Inselspital,BernUniversityHospital,Bern,Switzerland
JasonM.Berk
DepartmentofCellBiology,JohnsHopkinsUniversitySchoolofMedicine,Baltimore,
Maryland,USA
VeronikaBoczonadi
InstituteofGeneticMedicine,NewcastleUniversity,Newcastle-upon-Tyne,United
Kingdom
PascaleBomont
Atip-AvenirTeam,andINMInsermU1051,Universite´ deMontpellier,Montpellier,
France
LucaBorradori
DepartmentofClinicalResearch,UniversityofBern,andDepartmentofDermatology,
Inselspital,BernUniversityHospital,Bern,Switzerland
Jamal-EddineBouameur
DepartmentofClinicalResearch,UniversityofBern,andDepartmentofDermatology,
Inselspital,BernUniversityHospital,Bern,Switzerland
BenjaminBourgeois
InstituteforIntegrativeBiologyoftheCell,CEA,CNRS,Universite´ Paris-Sud,
Gif-sur-Yvette,Paris,France
xiii
xiv Contributors
BrigitteBuendia
InstitutdeBiologieFonctionnelleetAdaptative,Universite´ ParisDiderot,Paris,France
Rube´nM.Buey
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,andMetabolicEngineeringGroup,DepartmentofMicrobiologyandGenetics,
UniversityofSalamanca,Salamanca,Spain
ArturoCarabias
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
AnaM.Carballido
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
Hee-JungChoi
SchoolofBiologicalSciences,SeoulNationalUniversity,Seoul,SouthKorea
DonaldM.Coen
DepartmentofBiologicalChemistryandMolecularPharmacology,HarvardMedical
School,Boston,Massachusetts,USA
VictorE.Cruz
DepartmentofBiology,MassachusettsInstituteofTechnology,Cambridge,Massachusetts,
USA
Jose´ M.dePereda
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
AgnieszkaDobrzynska
AndalusianCenterforDevelopmentalBiology,CSIC-JuntadeAndalucia-Universidad
PablodeOlavide,CarreteradeUtrera,Seville,Spain
F.EsraDemircioglu
DepartmentofBiology,MassachusettsInstituteofTechnology,Cambridge,Massachusetts,
USA
BertrandFavre
DepartmentofClinicalResearch,UniversityofBern,andDepartmentofDermatology,
Inselspital,BernUniversityHospital,Bern,Switzerland
RicardoA.Figueroa
DepartmentofNeurochemistry,StockholmUniversity,Stockholm,Sweden
RadiaForteza
DepartmentofCellBiology,UniversityofMiamiMillerSchoolofMedicine,Miami,
Florida,USA
PeterFuchs
DepartmentofBiochemistryandCellBiology,MaxF.PerutzLaboratories,Universityof
Vienna,ViennaBiocenter(VBC),Vienna,Austria
Contributors xv
ChristelleGally
IGBMC,DevelopmentandStemCellsProgram,CNRS(UMR7104)/INSERM(U964)/
Universite´ deStrasbourg,Illkirch,France
SpiroGetsios
DepartmentofDermatology;DepartmentofCellandMolecularBiology,Northwestern
UniversityFeinbergSchoolofMedicine,andRobertH.LurieComprehensiveCancer
Center,NorthwesternUniversity,Chicago,Illinois,USA
Mar´ıaGo´mez-Herna´ndez
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
DmitryGoryunov
DepartmentofPathologyandCellBiology,TaubInstituteforResearchonAlzheimer’s
DiseaseandtheAgingBrain,ColumbiaUniversityCollegeofPhysiciansandSurgeons,
NewYork,USA
KathleenJ.Green
DepartmentofPathology;DepartmentofDermatology,NorthwesternUniversityFeinberg
SchoolofMedicine,andRobertH.LurieComprehensiveCancerCenter,Northwestern
University,Chicago,Illinois,USA
RalphGra¨f
InstituteforBiochemistryandBiology,DepartmentofCellBiology,UniversityofPotsdam,
Potsdam,Germany
YosefGruenbaum
DepartmentofGenetics,TheAlexanderSilbermanInstituteofLifeSciences,TheHebrew
UniversityofJerusalem,Jerusalem,Israel
InesHahn
FacultyofLifeSciences,MichaelSmithBuilding,Manchester,UnitedKingdom
EinarHallberg
DepartmentofNeurochemistry,StockholmUniversity,Stockholm,Sweden
JenniferC.Harr
DepartmentofBiologicalChemistryandCenterforEpigenetics,JohnsHopkinsUniversity,
Baltimore,MD,USA
IsalineHerrada
InstituteforIntegrativeBiologyoftheCell,CEA,CNRS,Universite´ Paris-Sud,
Gif-sur-Yvette,Paris,France
PaulHoover
DepartmentofDermatology,NorthwesternUniversityFeinbergSchoolofMedicine,
Chicago,Illinois,USA
Yu-ShanHuang
InstituteofMolecularMedicine,CollegeofLifeSciences,NationalTsingHuaUniversity,
Hsinchu,Taiwan
xvi Contributors
ArantzaInfante
StemCellsandCellTherapyLaboratory,BioCrucesHealthResearchInstitute,Cruces
UniversityHospital,Barakaldo,Spain
MohammedHakimJafferali
DepartmentofNeurochemistry,StockholmUniversity,Stockholm,Sweden
JeremyP.Kamil
DepartmentofBiologicalChemistryandMolecularPharmacology,HarvardMedical
School,Boston,Massachusetts,andDepartmentofMicrobiologyandImmunology,
LouisianaStateUniversityHealthSciencesCenter,Shreveport,Louisiana,USA
JenniferL.Koetsier
DepartmentofPathology,NorthwesternUniversityFeinbergSchoolofMedicine,Chicago,
Illinois,USA
RashmiKothary
RegenerativeMedicineProgram,OttawaHospitalResearchInstitute;Departmentof
CellularandMolecularMedicine;DepartmentofMedicine,UniversityofOttawa,and
UniversityofOttawaCenterforNeuromuscularDisease,Ottawa,Ontario,Canada
MichelLabouesse
IBPS,Paris,France
RonaldK.H.Liem
DepartmentofPathologyandCellBiology,TaubInstituteforResearchonAlzheimer’s
DiseaseandtheAgingBrain,ColumbiaUniversityCollegeofPhysiciansandSurgeons,
NewYork,USA
AnishaLynch-Godrei
RegenerativeMedicineProgram,OttawaHospitalResearchInstitute,andDepartmentof
CellularandMolecularMedicine,UniversityofOttawa,Ottawa,Ontario,Canada
ArtoMa¨a¨tta¨
SchoolofBiologicalandBiomedicalSciences,DurhamUniversity,Durham,
UnitedKingdom
AlexandrA.Makarov
WellcomeTrustCentreforCellBiology,UniversityofEdinburgh,Edinburgh,
UnitedKingdom
Jose´ A.Manso
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
AnastasiaMashukova
DepartmentofPhysiology,NovaSoutheasternUniversity,Ft.Lauderdale,andDepartment
ofCellBiology,UniversityofMiamiMillerSchoolofMedicine,Miami,Florida,USA
AaronA.Mehus
SanfordChildren’sHealthResearchCenter,SanfordResearch,SiouxFalls,SouthDakota,
USA
Contributors xvii
PeterMeinke
WellcomeTrustCentreforCellBiology,UniversityofEdinburgh,Edinburgh,United
Kingdom
IreneMeyer
InstituteforBiochemistryandBiology,DepartmentofCellBiology,UniversityofPotsdam,
Potsdam,Germany
EstherOrtega
InstitutodeBiolog´ıaMolecularyCelulardelCa´ncer,ConsejoSuperiordeInvestigaciones
Cient´ıficas,UniversityofSalamanca,Salamanca,Spain
Ming-DerPerng
InstituteofMolecularMedicine,CollegeofLifeSciences,NationalTsingHuaUniversity,
Hsinchu,Taiwan
AndreasProkop
FacultyofLifeSciences,MichaelSmithBuilding,Manchester,UnitedKingdom
RoyA.Quinlan
BiophysicalSciencesInstitute,UniversityofDurham,Durham,UnitedKingdom
KarenL.Reddy
DepartmentofBiologicalChemistryandCenterforEpigenetics,JohnsHopkinsUniversity,
Baltimore,MD,USA
Gu¨ntherA.Rezniczek
DepartmentofObstetrics&Gynecology,MarienHospitalHerne,Ruhr-Universita¨t
Bochum,Herne,Germany
AndreaRizzotto
WellcomeTrustCentreforCellBiology,UniversityofEdinburgh,Edinburgh,United
Kingdom
ClaraI.Rodr´ıguez
StemCellsandCellTherapyLaboratory,BioCrucesHealthResearchInstitute,Cruces
UniversityHospital,Barakaldo,Spain
MatthewRonshaugen
FacultyofLifeSciences,MichaelSmithBuilding,Manchester,UnitedKingdom
KyleJ.Roux
SanfordChildren’sHealthResearchCenter,SanfordResearch,andDepartmentof
Pediatrics,SanfordSchoolofMedicine,UniversityofSouthDakota,SiouxFalls,
SouthDakota,USA
Ine´sGarc´ıaRubio
CentroUniversitariodelaDefensa,AcademiaGeneralMilitar,Zaragoza,Spain
PedroJ.Salas
DepartmentofCellBiology,UniversityofMiamiMillerSchoolofMedicine,Miami,
Florida,USA
CamilleSamson
InstituteforIntegrativeBiologyoftheCell,CEA,CNRS,Universite´ Paris-Sud,Gif-sur-
Yvette,Paris,France
xviii Contributors
EricC.Schirmer
WellcomeTrustCentreforCellBiology,UniversityofEdinburgh,Edinburgh,United
Kingdom
ThomasU.Schwartz
DepartmentofBiology,MassachusettsInstituteofTechnology,Cambridge,Massachusetts,
USA
MayuriSharma
DepartmentofBiologicalChemistryandMolecularPharmacology,HarvardMedical
School,Boston,Massachusetts,USA
NataliaSa´nchez-Soriano
CellularandMolecularPhysiology,InstituteofTranslationalMedicine,Universityof
Liverpool,Liverpool,UnitedKingdom
SandraSzabo
DepartmentofBiochemistryandCellBiology,MaxF.PerutzLaboratories,Universityof
Vienna,ViennaBiocenter(VBC),Vienna,Austria
GernotWalko
CentreforStemCells&RegenerativeMedicine,FacultyofLifeSciencesandMedicine,
King’sCollegeLondon,London,UnitedKingdom
WilliamI.Weis
DepartmentofStructuralBiology,andDepartmentofMolecular&CellularPhysiology,
StanfordUniversitySchoolofMedicine,Stanford,California,USA
KarlL.Wo€genstein
DepartmentofBiochemistryandCellBiology,MaxF.PerutzLaboratories,Universityof
Vienna,ViennaBiocenter(VBC),Vienna,Austria
GerhardWiche
DepartmentofBiochemistry&CellBiology,MaxF.PerutzLaboratories,Universityof
Vienna,Vienna,Austria
KatherineL.Wilson
DepartmentofCellBiology,JohnsHopkinsUniversitySchoolofMedicine,Baltimore,
Maryland,USA
LilliWinter
InstituteofNeuropathology,UniversityHospitalErlangen,Erlangen,Germany
HowardJ.Worman
DepartmentofMedicine,andDepartmentofPathologyandCellBiology,Collegeof
PhysiciansandSurgeons,ColumbiaUniversity,NewYork,USA
HuiminZhang
JiangsuKeyLaboratoryofInfectionandImmunity,InstitutesofBiologyandMedical
Sciences,SoochowUniversity,Suzhou,Jiangsu,PRChina
SophieZinn-Justin
InstituteforIntegrativeBiologyoftheCell,CEA,CNRS,Universite´ Paris-Sud,Gif-sur-
Yvette,Paris,France
PREFACE
Proteins that bind to intermediate filaments come in hundreds of sizes and
“flavors.”Somearestructuralgiantsthatinterlinkthecytoskeleton.Others
resideattheinnernuclearmembrane,holdingcourtwithlaminsandsilent
genes. Many more remain hidden from view, their potential contributions
tocellsordiseaseunknown.Studyingsuchproteinsrequiresacutting-edge
toolkit of methods and expert advice, both featured in this volume of
Methods in Enzymology.
Rouxandcolleagues(Chapter1)detailapowerfulandbroadlyapplica-
blemethod,biotinylationidentification(BioID),toidentifyproteinslocated
within 10nm of a BioID-fusion protein in living cells. These “proximal”
proteins include direct in vivo partners or associated protein complexes, as
demonstrated for the nuclear intermediate protein, lamin A. Gra¨f and col-
leaguessuccessfullymodifiedtheBioIDtoolkitforuseinDictyostelium,now
enabling studies of intermediate filament-associated proteins in this evolu-
tionarily diverse organism (Chapter 2). Taking “lamin association” to an
entirely new level, Harr and Reddy detail their state-of-the-art new TCIS
method to study how specific segments of DNA or chromatin-associated
proteins drive intranuclear movement to lamins and the nuclear lamina
(Chapter 21).
Proteins that bind lamins are exceedingly diverse. Schirmer and col-
leagues provide insights into the many biochemical and functional features
thatshouldbeconsideredwhenexpressinganemergingspectrumoflamin-
bindingnuclearmembraneproteinsasrecombinantpolypeptidesinbacteria
(Chapter 5). Successful methods for purification and structural analysis are
provided for specific lamin-binding proteins. These include SUN-domain
and KASH-domain proteins, which form LINC complexes that transduce
force across the nuclear envelope (Schwartz and colleagues, Chapter 4),
as well as LAP2, emerin and MAN1, which share the eponymous LEM-
domainfoldandalsohaveunstructuredregions(Zinn-Justinandcolleagues,
Chapter 3). Beyond proteins, Coen and colleagues describe how to purify
entire “nuclear egress” complexes formed by the human cytomegalovirus,
which include lamin-associated proteins (Chapter 25).
Advancesinthepurificationandstructuralanalysisofchallenginglylarge
cytoplasmic proteins are provided for plectin and BPAG1e (de Pereda and
colleagues, Chapter 10) and desmoplakin (Choi and Weis, Chapter 11).
xix
xx Preface
Functional assays are providing significant insight into the biological
roles of cytoplasmic intermediate filament binding proteins, including
molecular chaperones (Salas and colleagues, Chapter 8; Quinlan and col-
leagues, Chapter 9) and gigaxonin, an E3 ubiquitin ligase involved in the
degradation of intermediate filament proteins (Bomont, Chapter 12).
Borradori and colleagues describe a new GFP-based binding assay to study
plakin association with intermediate filaments (Chapter 7). Green and col-
leagues use a 3D culture model to advance the functional interrogation of
theintermediatefilament-desmosomescaffoldduringkeratinocytedifferen-
tiation (Chapter 15). Boczonadi and Ma¨a¨tta¨ discuss general approaches to
study the function of periplakin and envoplakin in cell culture models
and gene-targeted mice (Chapter 16). The functional diversity of lamin-
associated proteins is reflected in protocols to separate functionally distinct
populationsoflamin-bindingproteins(BerkandWilson,Chapter6),iden-
tify transcription factors relevant to prelamin A pathology (Infante and
Rodr´ıguez, Chapter 23), and identify novel protein–protein interactions
atthenuclearenvelopeviachemicalcross-linking(Hallbergandcolleagues,
Chapter 24).
Geneticmethodsareincreasinglyimportanttounderstandintermediate
filamentbiologyandareexpandingbeyondmice.ThisvolumeofMethodsin
Enzymologyincludesstate-of-the-artprotocolstostudylamin-bindingpro-
teins in Caenorhabditis elegans, which has one lamin gene (Gruenbaum and
colleagues, Chapter 22), and to study the complex functions of the single
spectraplakin locus in either C. elegans (Labouesse and colleagues,
Chapter 20) or Drosophila (Prokop and colleagues, Chapter 19). Other
chapters describe increasingly sophisticated use of mouse genetics to study
the roles of plectin in skin and muscle (Wiche and colleagues, Chapter 13),
epiplakin in epithelial cells (Fuchs and colleagues, Chapter 14), BPAG1 in
neurons (Lynch-Godrei and Kothary, Chapter 18), and microtubule-actin
cross-linkingfactor1intheskin,heart,nervoussystem,andintestinalepithelia
(Goryunov and Liem, Chapter 17). We sincerely hope these protocols will
help your research advance.
ARNOUD SONNENBERG AND KATHERINE L. WILSON
Division of Cell Biology,
The Netherlands Cancer Institute, Amsterdam, The Netherlands
Department of Biology, The Johns Hopkins
University School of Medicine, Baltimore Maryland, USA