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ANNUALPLANTREVIEWS VOLUME46
ANNUALPLANTREVIEWS
PlantNuclearStructure, GenomeArchitecture andGeneRegulation
Editedby
DavidE.Evans
DepartmentofBiologicalandMedicalSciences
OxfordBrookesUniversity,Oxford,UK
KatjaGraumann
DepartmentofBiologicalandMedicalSciences
OxfordBrookesUniversity,Oxford,UK
JohnA.Bryant
Biosciences,UniversityofExeter,Exeter,UK
Thiseditionfirstpublished2013. C 2013byJohnWiley&Sons,Ltd
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FirstImpression2013
AnnualPlantReviews
Aseriesforresearchersandpostgraduatesintheplantsciences.Eachvolume inthisseriesfocusesonathemeoftopicalimportanceandemphasisisplaced onrapidpublication.
EditorialBoard:
Prof.JeremyA.Roberts (Editor-in-Chief),PlantScienceDivision,Schoolof Biosciences,UniversityofNottingham,SuttonBoningtonCampus,Loughborough,Leicestershire,LE125RD,UK; Prof.DavidE.Evans, DepartmentofBiologicalandMedicalSciences,Oxford BrookesUniversity,HeadingtonCampus,OxfordOX30BP,UK; DrMichaelT.McManus, InstituteofMolecularBioSciences,MasseyUniversity,PalmerstonNorth,NewZealand; DrJocelynK.C.Rose, DepartmentofPlantBiology,CornellUniversity, Ithaca,NewYork14853,USA.
Titlesintheseries:
1.Arabidopsis
EditedbyM.AndersonandJ.A.Roberts
2.BiochemistryofPlantSecondaryMetabolism
EditedbyM.Wink
3.FunctionsofPlantSecondaryMetabolitesandtheirExploitationin Biotechnology
EditedbyM.Wink
4.MolecularPlantPathology
EditedbyM.DickinsonandJ.Beynon
5.VacuolarCompartments
EditedbyD.G.RobinsonandJ.C.Rogers
6.PlantReproduction
EditedbyS.D.O’NeillandJ.A.Roberts
7.Protein–ProteinInteractionsinPlantBiology
EditedbyM.T.McManus,W.A.LaingandA.C.Allan
8.ThePlantCellWall
EditedbyJ.K.C.Rose
9.TheGolgiApparatusandthePlantSecretoryPathway
EditedbyD.G.Robinson
10.ThePlantCytoskeletoninCellDifferentiationandDevelopment
EditedbyP.J.Hussey
11.Plant–PathogenInteractions
EditedbyN.J.Talbot
12.PolarityinPlants
EditedbyK.Lindsey
13.Plastids
EditedbyS.G.Moller
14.PlantPigmentsandtheirManipulation
EditedbyK.Davies
15.MembraneTransportinPlants
EditedbyM.R.Blatt
16.IntercellularCommunicationinPlants
EditedbyA.J.Fleming
17.PlantArchitectureandItsManipulation
EditedbyC.G.N.Turnbull
18.Plasmodeomata
EditedbyK.J.Oparka
19.PlantEpigenetics
EditedbyP.Meyer
20.FloweringandItsManipulation
EditedbyC.Ainsworth
21.EndogenousPlantRhythms
EditedbyA.HallandH.McWatters
22.ControlofPrimaryMetabolisminPlants
EditedbyW.C.PlaxtonandM.T.McManus
23.BiologyofthePlantCuticle
EditedbyM.Riederer
24.PlantHormoneSignaling
EditedbyP.HaddenandS.G.Thomas
25.PlantCellSeparationandAdhesion
EditedbyJ.R.RobertsandZ.Gonzalez-Carranza
26.SenescenceProcessesinPlants
EditedbyS.Gan
27.SeedDevelopment,DormancyandGermination
EditedbyK.J.BradfordandH.Nonogaki
28.PlantProteomics
EditedbyC.Finnie
29.RegulationofTranscriptioninPlants
EditedbyK.Grasser
30.LightandPlantDevelopment
EditedbyG.Whitelam
31.PlantMitochondria
EditedbyD.C.Logan
32.CellCycleControlandPlantDevelopment
EditedbyD.Inz ´ e
33.IntracellularSignalinginPlants
EditedbyZ.Yang
34.MolecularAspectsofPlantDiseaseResistance
EditedbyJ.Parker
35.PlantSystemsBiology
EditedbyG.M.CoruzziandR.A.Guti ´ errez
36.TheMoss Physcomitrellapatens
EditedbyC.D.Knight,P.-F.PerroudandD.J.Cove
37.RootDevelopment
EditedbyT.Beeckman
38.FruitDevelopmentandSeedDispersal
EditedbyL.Østergaard
39.FunctionandBiotechnologyofPlantSecondaryMetabolites
EditedbyM.Wink
40.BiochemistryofPlantSecondaryMetabolism
EditedbyM.Wink
41.PlantPolysaccharides
EditedbyP.Ulvskov
42.NitrogenMetabolisminPlantsinthePost-genomicEra
EditedbyC.FoyerandH.Zhang
43.BiologyofPlantMetabolomics
EditedbyR.D.Hall
44.ThePlantHormoneEthylene
EditedbyM.T.McManus
45.TheEvolutionofPlantForm
EditedbyB.A.AmbroseandM.D.Purugganan
2.9TheplantNEinmeiosis
2.11.1Nucleirepositioninginresponseto
2.11.2FunctionsoftheplantNEduringviralinfection47
XiaoZhou,JoannaBorucandIrisMeier
MartinW.Goldberg
4.7Isthereatrans-nuclearenvelopecomplexinplantsthat linksthenucleoskeletontothecytoskeleton?
4.8Roleofthenuclearlaminaaspartofthenucleoskeleton102
4.9Structuralevidenceforthenucleoskeleton
4.10NuMAinplants
4.11Matrixattachmentregions(MARs)andtheroleofthe nucleoskeletoninchromatinorganization
4.12Chromocentresandtheplantnucleoskeleton
4.13Longcoiled-coilproteinsinplantsandtheirroleinnuclear organization:candidatesforplaminsandnucleoskeletal proteins?
4.14Actinandmicrotubulesinthenucleus
4.15Conclusions
5GenomicsandChromatinPackaging
5.1Chromatincomponentsandstructureinhighereukaryotes123
5.2Histonesandnucleosomefibre
5.2.1Histonevariants
5.2.2Histonemodifications
5.2.3Nucleosomedynamics
5.3Linkerhistoneandthehigherorderchromatin-orderfibre138
5.3.1Theelusivehigherorderchromatinfibre
EmmanuelVanrobays,M ´ elanieThomasandChristopheTatout 6.1Heterochromatinstructure
6.1.3Non-histoneproteinbinding
6.1.4Heterochromatinisanepigeneticstate
6.2Heterochromatinorganization
6.2.1Heterochromatinandnucleararchitecture
6.2.2Recruitmentofheterochromatinatthenuclear periphery
6.2.3Higherorderofchromatinorganization
6.3Functionalsignificanceofheterochromatinpositioning176
6.3.1Centricheterochromatindirectschromosome
6.3.2Spatialpositioningofheterochromatinaffects transcriptionalactivity178
6.3.3Heterochromatinpositioningprotects againstgenomeinstability179 6.4Perspectives180
7TelomeresinPlantMeiosis:TheirStructure,Dynamics andFunction
NicolaY.Roberts,KimOsman,F.ChrisH.Franklin,MonicaPradillo, JavierVaras,JuanL.SantosandSusanJ.Armstrong 7.1Introduction
7.2.1Telomerebindingproteins
7.2.2Arabidopsistelomerebindingproteins
7.2.3DNArepairproteins
7.3Thebehaviourofthetelomeresinmeiosis
7.3.1Thebouquet
7.3.2Aroleforthebouquet
7.4.1Meiosisin A.thaliana telomere-deficientlines206
7.5HowarethetelomeresmovedinmeioticprophaseI?208
7.5.1Colchicinedisruptsmeioticprogression
7.5.2Theroleofactinintelomeremovement
7.6Componentsofthenuclearenvelope
7.7Componentsoftheplantnuclearenvelope
8TheNuclearPoreComplexinSymbiosisandPathogenDefence229
AndreasBinderandMartinParniske 8.1Introduction
8.2Thenuclearporeandplant-microbesymbiosis
8.2.1Commonsignallinginarbuscularmycorrhizaand root-nodulesymbiosis
8.2.2Symbioticsignallingatthenucleus
8.2.3Symbioticdefectsin ljnup85,ljnup133 and nena mutants
8.2.4Howdonucleoporinsfunctionin plant-microbesymbiosis?
8.3Thenuclearporeandplantdefence
8.3.1Plantimmuneresponsescanbetriggeredby pathogen-associatedmolecularpatternsand microbialeffectors 235
8.3.2AtNUP88andAtNUP96arerequiredforbasaland NB-LRR-mediatedplantimmunity 236
8.3.3Mechanismsofnucleoporin-mediatedplant defencesignalling 237
8.4Specificity,redundancyandgeneralfunctionsofplant nucleoporins 239
8.4.1TheNUP107-160sub-complex
8.4.2Hormonesignalling
8.4.3Development,floweringtime,stresstoleranceand RNAtransport
8.5Challengesandconclusion
Colorplate(betweenpages104and105)
LISTOFCONTRIBUTORS
SusanJ.Armstrong SchoolofBiosciences
UniversityofBirmingham
B152TT UK
AndreasBinder FacultyofBiology,Genetics,UniversityofMunich(LMU) GroßhadernerStraße4 82152Martinsried Germany
JoannaBoruc DepartmentofMolecularGenetics
TheOhioStateUniversity Columbus OH43210 USA
JohnA.Bryant Biosciences
UniversityofExeter Exeter
EX44QD,UK
DavidE.Evans DepartmentofBiologicalandMedicalSciences FacultyofHealthandLifeSciences
OxfordBrookesUniversity HeadingtonCampus Oxford
OX30BP UK
F.ChrisH.Franklin SchoolofBiosciences
UniversityofBirmingham
B152TT UK
MartinW.Goldberg
DepartmentofBiologicalandBiomedicalSciences UniversityofDurham
Durham
DH13LE UK
KatjaGraumann DepartmentofBiologicalandMedicalSciences FacultyofHealthandLifeSciences
OxfordBrookesUniversity HeadingtonCampus
Oxford OX30BP UK
IrisMeier DepartmentofMolecularGenetics
TheOhioStateUniversity Columbus
OH43210 USA
EugenioSanchez-Moran SchoolofBiosciences UniversityofBirmingham
B152TT UK
KimOsman SchoolofBiosciences UniversityofBirmingham
B152TT
UK
MartinParniske FacultyofBiology,Genetics UniversityofMunich(LMU) GroßhadernerStraße4 82152Martinsried Germany
MonicaPradillo DepartmentodeGenetica FacultaddeBiologia UniversidadComplutense
Madrid
28040Spain
NicolaY.Roberts SchoolofBiosciences UniversityofBirmingham
B152TT UK
JuanL.Santos DepartmentodeGenetica FacultaddeBiologia UniversidadComplutense
Madrid 28040Spain
ChristopheTatout GReDLaboratory
UMRCNRS6293
INSERMU1103
UniversityBlaisePascal
Aubi ` ere
France
M ´ elanieThomas GReDLaboratory
UMRCNRS6293
INSERMU1103
UniversityBlaisePascal
Aubi ` ere
France
EmmanuelVanrobays GReDLaboratory
UMRCNRS6293
INSERMU1103
UniversityBlaisePascal
Aubi ` ere
France
JavierVaras DepartmentodeGenetica
FacultaddeBiologia
UniversidadComplutense
Madrid
28040Spain
XiaoZhou
DepartmentofMolecularGenetics
TheOhioStateUniversity
Columbus OH43210 USA
PREFACE
Thisvolumewasconceivedtobringtogetherreviewsdescribingrecent advancesinknowledgeandunderstandingofplantnuclearstructuresand functions,includingthatofthenuclearenvelope.Thebookisparticularly timelyinthatrecentprogresshasbeenrapidinkeyareasincludingdescriptionandcharacterizationofproteinsofthenuclearenvelopeandnuclear porecomplex,novelinsightsintonucleoskeletalstructures,aswellasdevelopmentsrelatedtochromatinorganization,functionandgeneexpression. Togethertheseadvancesprovideaframeworkforcomparativeunderstandingofnuclearenvelopestructureandfunctioninarangeoforganismsand forunderstandingitsevolution.
CurrentknowledgeofthedynamicstructureofplantDNAandchromatin isdiscussedbySanchez-MoraninChapter5.Despiteintensivestudyof histonesandotherchromosome-associatedproteins,interactionstoachieve thecomplexstructuresrequiredbothininterphaseandduringcelldivision remainpoorlyunderstood.Thestructuresrequireseverallevelsoforganization,thefirstbeingthenucleosomalfibrecomprisingDNAwrappedaround acoreofhistones.Thisisadynamicstructureandmechanismsforitsremodellingaredescribed.Thenucleosomalfibreisthenwoundintoastructure termedthechromatinfibre,whichisarrangedinloopsassociatedwitha multi-proteinchromosomescaffold,thethirdlevelofstructure.Thisinterphasestructureundergoesrapiddynamicchangeinmitosiswithfurther condensationforreplicationanddivision.Theimportanceofthestructural organizationofchromatinforprocessessuchastranscription,replication, repair,recombination,condensationandsegregationisalsodiscussed.Asin metazoans,plantchromatinisorganizedintoregionsofhetero-andeuchromatinwithheterochromatinadjacenttotheNE.
Recentadvancesinunderstandingheterochromatinstructurearepresented inChapter6byVanrobays etal. Heterochromatin,originallythoughtto becondensed,gene-poorand‘silent’,isnowknownoftentobepreferentiallylocalizedtothenuclearenvelopeandnucleolusanditssignificance isbecomingclearasanepigeneticstaterequiredformanyfunctionsofthe genome,includinggeneregulation,segregationofchromosomesandmaintainingstabilityofthegenome.Despitelimitedknowledgeofit,inmost speciesheterochromatinisthemainformofchromatinandkeyquestions remaintobeanswered.HowisspatialorganizationofheterochromatinmaintainedthroughthecellcycleasDNAisreplicated,chromatincondensed,and thenuclearenvelopedisruptedandreformed?Interactionsbetweennuclear
envelope,nucleoskeletonandchromatinarelikelytobeverysignificantand arediscussedtogetherwithothertheoriesforheterochromatinpositioning.
Plantgenomesvarygreatlyinsizebutinallcasesthegenomeiscontainedwithinaverysmallcompartmentanditisclearthatcomplexthreedimensionalorganizationisneededinorderforthemanyprocessesrequired forfunction.Thisthree-dimensionalstructurerequiresinteractionsbetween chromatin,theenvelope,thenuclearporesandtherestofthecell.InChapter4,Goldbergdiscussesfromanultrastructuralandbiochemicalperspective thepresenceofanequivalentofthehighlyorderedlaminaandnucleoskeleton describedinmetazoans.Suchastructureappearstoberequiredfornuclear function,butuntilrecentlyitsproteincompositionhaseludedplantscientists. Plantcellshavenoproteinshomologoustothelaminsorotherintermediate filamentprotein.RecentelectronmicroscopestudiesinGoldberg’slaboratory oftheinnerfaceoftheplantnuclearenveloperevealafilamentousstructure interconnectingtheNPCs.Thisappearstobeorganizedsimilarlytothelaminaof Xenopus oocytes.Proteincandidatesforaplantnucleoskeletonhave recentlybeensuggestedfromanumberofapproaches;theselongcoiled-coil nuclear-localizedproteinsshowsomesimilaritiestonucleoskeletalproteins ofthemetazoansandGoldbergpresentsthegrowing,butasyetincomplete, evidencefortheirrole.Thelikely(directorindirect)interactionsoftheseproteinswiththeproteinsofthenuclearenvelopeviaa‘LinkerofNucleoskeletonandCytoskeleton’complexisalsoconsideredinChapter2byGraumann andEvans.Therein,theauthorsdescribethat,incommonwithmetazoans, plantshaveonekeyfamilyofproteinsthatinotherkingdomsconstitutes theinnernuclearenvelopecomponentofthisbridgingcomplex,namelythe Sad1/Unc84(SUN)-domainproteinfamily.Absenceofavarietyofother innernuclearenvelopecomponentsinvolvedinnuclearenvelope-chromatin interactionsinotherkingdomssuggeststhattheSUN-domainproteinsplay aparticularlysignificantandbroaderroleinplants.Inmanyrespectshowever,thehigherplantSUN-domainproteinsshowremarkableconservation instructuretothoseofotherorganisms.Theyaresmallerthantheirmetazoan counterparts,beingclosestinsizetotheyeasthomologueSad1.Inaddition, theauthorsdiscussfirstevidenceofproteinsinteractingwithSUN-domain proteinsinplantsthatshowsimilarityinstructureandmechanismtothe Klarsicht/Anc-1/SyneHomology(KASH)-domainproteinsofotherkingdoms,whichcompletethenucleo-cytoskeletalbridgingcomplexes.Chapter2 alsofocusesonotherproteincomponentsoftheplantnuclearenvelopeas wellasitslipidcompositionandhighlightsmanyofthecellularandnuclear processesinwhichtheplantnuclearenvelopeplayskeyroles.
Structureandpositionofchromosomesmustbeachievedbothforsuccessfulmitosisandmeiosis.EvidenceforSUN-domainproteininvolvementin thebreakdownandreformationofthenuclearenvelopeinplantmitosisis presentedinChapter2togetherwithsuggestionsofconservedmechanisms betweenkingdoms.Meiosis,whilemorecomplex,hasreceivedconsiderable attentionandtheroleoftelomeresispresentedbyRoberts etal. inChapter7,
whorevealemergingevidencefortheirroleinearlyeventsinthemovementandsynapsisofhomologouschromosomes.StudiesinArabidopsis suggestthatpairedtelomereslooselyclusteratthenuclearperipheryinmeioticprophase1;itissuggestedthatthisfacilitateschromosomealignment andsynapsis.Theproteinsinvolvedintheattachmentoftelomerestothe nuclearenveloperemainelusive;however,incommonwiththeyeastand metazoans,aroleforSUN-domainproteinsissuggested.Explorationofthe structuralproteininteractionsinmeiosisisbeingvigorouslypursued.
Recentcharacterizationofproteinsoftheplantnuclearporecomplex(NPC) hasrevealedthatthestructuremorecloselyresemblesthoseofvertebrates thanyeastorfungi.InChapter3,Zhou etal. describethesignificantprogress maderecentlyinidentifying30constituentproteinsoftheplantNPCaswell ascharacterizingplantNPCstructure.WhiletheoverallarchitectureofNPCs isconservedineukaryotes,theplantNPCaresetapartbyseveralunique featuresandabsenceofanumberofvertebratenucleoporins.Significantly, theanchorageofRanGAP,involvedinthegenerationoftheRanGTP/GDP gradientrequiredfornuclearimportandexport(amechanismconserved betweenkingdoms)hasbeenshowntodiffersignificantlybetweenplants andotherorganisms.Inmammals,forinstance,RanGAPisanchoredtothe porecomplexbysumoylation.Inplants,thisfunctionistakenoverbyinteractionwithproteinsassociatedwiththenuclearporecomplextermedtheWPP (tryptophanprolineproline)interactingproteins(WIPs)andWPPinteracting tail-anchoredproteins(WITs).Apartfromstructuraldifferences,theauthors alsodiscussplant-specificfunctionsandnon-traffickingprocessesthatplant nucleoporinsareinvolvedin,includingmitoticfunctions,plantdevelopment, hormoneandabioticstressresponsesandplant-microbeinteractions.ThelattertopicistheprimaryfocusofChapter8byBinderandParniske.Using Lotus japonicus asamodelsystem,lossoffunctionmutantsofseveralnucleoporins resultinimpairedmycorrhizalassociationaswellasroot-nodulesymbiosis linkedtofailureofnuclearcalciumsignalling.In Arabidopsisthaliana, nucleoporinshavebeenshowntoberequiredforthetwomajorformsofresponseto fungalpathogens,namelypathogen-associatedmolecularpattern(PAMP)triggeredanddiseaseresistance(R)gene-mediateddefencesignalling.Thisis presentedinthecontextofexpandingknowledgeofthenuclearporecomplex andotherproteinsofthenuclearenvelopeandsuggestsimportanttargets forattentioninrelationtotheintroductionofnitrogenfixationintocereals andinthedevelopmentofcropsshowingenhancedresistancetofungi.The authorsalsofocusonthechallengesofcorrelatingspecificfunctionswith individualnucleoporinsduetothecomplexityofinteractionsandfunctions ofNPCcomponentsandfunctionalredundancies.
Itisevidentthatexplorationofplantnuclearstructure,genomearchitectureandgeneregulationhaswidespreadimplicationsforcropimprovement andfoodsecurity.MovementofthenucleusoccurringasstressanddevelopmentalresponsesarepresentedinChapter2byGraumannandEvans andincludemovementinintenselight,duetotouchandviralandfungal
infection.Suchmovementsarelikelytobesignificantinplanttoleranceto stressandinfectionandtoinvolvenucleo-cytoskeletalbridgingcomplexes atthenuclearenvelope.Thepositionaleffectsofchromatinstructureand thestructureofthenucleusongeneexpression,discussedinChapter6by Vanrobays etal., suggestanareawithconsiderablepotentialforexploration astoolstostudygenetargetingtosubnuclearlocalizationsbecomeavailable. Ithasyettobeestablishedwhetherlocalizationtothenuclearperiphery, porecomplexorotherregionsofthenucleusinducesarepressiveoractivationeffectinrespecttogeneexpression.Sucheffects,ifreproducible,have considerablepotentialfordevelopment.Perhapsthemostcomprehensively studiedrolefortheplantnuclearstructureswithwidespreadsignificance concernstheroleofthenuclearporecomplexinfungalpathogenesisand symbiosis.
Thereisaveryclearneedtoexpandknowledgeofproteininteraction networksatthenuclearenvelopeinvolvingcytoskeleton,nucleoskeletonand chromatincomponents.Studyofthenuclearenvelopeproteomehasbeen heldbackbyacombinationoflimitedinterestbyresearchersandthetechnical difficultiesofisolatingandanalysingit.Recentadvances–theidentification ofSUNdomainproteinsandfirstevidenceforalinkerofnucleoskeletonand cytoskeletoncomplex,thecharacterizationofmorethan30nucleoporinsand increasingfunctionalevidenceandthetentativecharacterizationofaplant lamina–allprovideaframeworkforrapidadvancescoupledwithincreased understandingofchromatinstructureandfunction.Giventheoutstanding importanceofthenucleusandofepigeneticfactors,weanticipatethatthe studyofplantnuclearstructure,genomearchitectureandgeneregulation willplayaverysignificantroleinthenearfuture.
Asknowledgeandunderstandingofthestructureandpropertiesof thenucleusandnuclearenvelopeexpand,wecometantalizinglycloser tounderstandingtheoriginsofthestructuresoftheeukaryoticcell.John Bryant(Chapter1)usestheinformationpresentedtogetherwithknowledge ofreplicationofnuclearDNAandtheimportofthereplicationproteinsto presentanddevelopcurrenttheoriesoftheoriginsofthenucleusandits envelope.Theearlypresenceofthenucleusandnucleoskeleton,predating thearrivalofchloroplastsandmitochondriaintheproto-eukaryoticcelland theprobableformationofthenuclearenvelopefrominvaginationsofthe plasmamembranearediscussedinthelightofthedevelopmentofkeyfeaturesofthehigherplantnucleus.Justaswehopethatpresentingadvancesin understandingthestructureandfunctionoftheplantnucleuswillstimulate researchinthisfield,itisequallyourhopetheseadvanceswillresultin betterappreciationoftheiroriginsnotonlyinplantsbutacrosstheordersof livingthings.
ACKNOWLEDGEMENTS
TheeditorswishtoacknowledgethecontributionofProfessorJ.S.(Pat) Heslop-HarrisonandDrTrudeSchwarzacher,DepartmentofBiology,UniversityofLeicester,UKtotheinceptionanddevelopmentofthisvolume. Theyalsowishtorecognizethecontributionofcolleaguesworkingonthe nuclearenvelopeandonnuclearstructureandfunctionwhoseresearchprovidedinspirationfortheworkpresentedhere.DEandKGacknowledgethe supportoftheLeverhulmeTrustundergrantF/00382/HandforanEarly CareerFellowshipforKG.
AnnualPlantReviews (2013) 46,1–18
http://onlinelibrary.wiley.com doi:10.1002/9781118472507.ch1
Chapter1 INTRODUCTION:MYSTERIES, MOLECULESAND MECHANISMS
JohnA.Bryant Biosciences,UniversityofExeter,Exeter,UK
Abstract: Thisbriefchaptermentionsthemainstructuralandfunctionalfeatures ofplantnucleiandindoingso,providesaverygeneralintroductiontootherchaptersinthebook.Italsocoversaspectsthatarenotfeaturedelsewhere,especiallythe replicationofnuclearDNAandtheimportofthereplicationproteins.Throughout thechapterthereisanunderlyingthemeofevolution,relatingbothtothesimilaritiestoanddifferencesfromtheArchaeaandtothepossibleevolutionaryorigins ofthenucleus.
Keywords: Archaea;DNAreplication;evolution;nuclearenvelope;nuclearlocalizationsignal;origin;proteinimport
1.1DarwinandMargulisrevisited
InafamouslettersentinJuly1879toJosephHooker,theDirectorofKew Gardens,CharlesDarwindescribedtheoriginofthefloweringplantsas‘an abominablemystery’.Over130yearslater,themysteryseemstobesolved, ifnotindetail,atleastingeneralterms.Itisnowthoughtthatflowering plantsdivergedfromalineageofseedferns(nowatotallyextinctgroup) inthelateJurassicorearlyCretaceousperiod(Doyle,2006,2008).Based onextensivephylogeneticanalysis,thelivingplantthatmostresemblesthe earliestangiosperms(i.e.whichisatthebaseoftheangiospermphylogenetic tree)is Amborellatrichopoda,asemi-climbingshrubonlyfoundintherain forestsofNewCaledonia.So,whileasolutiontothatmysteryhasbeen found,afurther,andperhapsmorefundamentalmysteryremains.Itisa
AnnualPlantReviewsVolume46:PlantNuclearStructure,GenomeArchitectureandGeneRegulation, FirstEdition.EditedbyDavidE.Evans,KatjaGraumannandJohnA.Bryant.
C 2013JohnWiley&Sons,Ltd.Published2013byJohnWiley&Sons,Ltd.
mysterythatinvolvesnotjustfloweringplantsbutalleukaryotesandatthe beginningofthe21stcenturyitisstillnotcompletelysolved.Thatmystery istheoriginofthenucleus,theorganellethatisthesubjectofthisbook. Asisevidentinsubsequentchapters,wehaveextensiveknowledgeofits structureandactivities.Itisatrulybeautifulorganelle–onethatinducesin manyofusasenseofwonder.However,wearenotatallsurewhereitcame fromalthough,aswillbecomeclearlaterinthechapter,afewhypothesesare beginningtoemergeasfrontrunners.
Onthequesttosolvethepuzzle,onefactortoconsideristheoriginof eukaryotes.Itisnowacceptedthatthetwoothermajormembrane-bound organelles,mitochondriaandchloroplasts,haveevolvedfrombacterialsymbiontsthatinvadedorwereengulfedbywhatwecouldcallproto-eukaryotes (asoriginallyproposedbyMargulis,1971a,b,1981).Thisideahasbeen extensivelyconfirmedbygenomicandproteomicstudies,whichalsosuggeststronglythatthoseproto-eukaryotichostcellswerederivedfromthe Archaeaand,intermsofenergymetabolism,wereusingaformofglycolysis1 .Further,itisclearthatfollowingtheendosymbioticevents,transferof genesfromboththenon-photosynthetic(i.e.mitochondrial)andthephotosynthetic(chloroplastic)endosymbiontstothehost’sgenomeoccurredon alargescale.Indeed,thattheprocessisstillgoingon(Huang etal.,2004, Rousseau-Gueutin etal.,2011,Wang etal.,2012).Butwhere,andinwhatstate werethegenomesofthoseproto-eukaryotichostorganisms?
Itwasthoughtforseveralyearsthatrelevantinformationcouldbeobtained bystudyofamitochondrialeukaryotes,eukaryotespresumedtodatebackto beforethefirstendosymbioticevent.However,itisnowknownthattheseare secondarilyamitochondrial,asrevealedbythepresenceofendosymbiontderivedgenesinthenucleusandthevestigesofamitochondrion(e.g.van derGiezenandTozar,2005;Minge etal.,2009).So,thesecellscannottellus whattheproto-eukaryotelookedlike.Nevertheless,itisclearthatinmore recentinstancesofgenetransfer(asmentionedabove),theorganellegene hasbeenintegratedintoatypicaleukaryoticnucleargenomelocatedina typicaleukaryoticnucleus.Thesestructuresarenohindrancetogenetransfer. Further,theuseofbioinformaticscoupledwithcomparativecellphysiology andbiochemistryinattemptsto‘root’theeukaryoticphylogenetictreeall leadtotheconclusionthatmostoftheapproximately60differencesbetween eukaryotesandprokaryotesweredevelopedordevelopingbeforethefirst symbioticevent,theacquisitionofmitochondria(deDuve,2007;Margulis etal.,2007;Cavalier-Smith,2009).
Theeukaryoticfeaturespossessedbytheproto-eukaryotesarethoughtto haveincludedthepossessionofanucleus,nucleoskeletonandcytoskeleton (Margulis etal.,2007;deDuve,2007;Cavalier-Smith,2009).Lookingatthe
1 ButnotethatinmodernArchaeathereareseveralvariantsofthe‘conventional’ glycolysispathway(SatoandAtomi,2011).
firsttwoofthese,thesedatadonotprovideanyclearcluesaboutwhere thenucleuscamefromandtherearealsoquestionsaboutthenatureofthe nucleoskeletonintheearliesteukaryotes.Focussingspecificallyonthisproblem,wenotethatafterthefirstsymbioticevent(acquisitionofmitochondria), theeukaryoticlineagesplitintotwomajorbranches(Cavalier-Smith,2002), theunikonts(withoneflagellum)thatgaveriseto,amongstotherthings, fungiandMetazoa,andthebikonts(withtwoflagella),onelineageofwhich becameplantsbytheacquisitionofchloroplasts(asmentionedabove;see alsoKeeling,2010).
Turningnowtolookatextantlineages,asisshowninChapters2and4,part ofthenucleoskeletoninanimalsistheprominentlamina,consistingmainly ofproteinsknownaslamins.However,plantslacklaminsbutdopossessa lamina-likestructurethathasbeencalledthe‘plamina’(Fiserova etal.,2009), consistingofplant-specificproteinsthatarefunctionalanaloguesoflamins. Finally,infungi,atleastasrepresentedbyyeasts,thenucleoskeletondoes nothaveanyformoflamina.So,basedontheoriginsofthesegroups,itis suggestedthattheproto-eukaryoticnucleoskeletonlackedalaminaandthat thishasdevelopedsubsequenttotheuni-kont/bikontsplit.Thisgivesusa littlemoreinformationontheearlynucleus,butthequestionofitsorigin remains.
Atthispointfurtherspecificdiscussionoftheoriginofnucleusisdeferred totheendofthechapter,althoughitwillappearmoreindirectlyfromtimeto timeinthenextthreesections.Attentionisnowturnedtothegenomeitself. Particularfocuswillbeplacedonthegeneralstructureofthegenome,on itsreplicationandontheimplicationsforthelatterprocessofenclosingthe genomeinanorganelle.
1.2Nuclei–generalfeatures
Inplantcellsthatarenotextensivelyvacuolated,thenucleusisthelargestand usuallythemostobviousorganelle.Eveninmaturecellswithlargevacuoles, thenucleusisusuallyclearlyvisiblewithinthecytoplasm.Itistheorganelle thatcontainsthebulkofthecell’sDNA,thenucleargenome.Indeed,chromatin(Chapters5and6),consistingmainlyofacomplexofDNAandproteins,isusuallythemostobviouscomponentofthenucleus.Thechromatin isattached via scaffold-ormatrix-associatedregions(SARs/MARs)tothe nuclearmatrix/scaffold/nucleoskeleton(Chapters4to6).Withinchromatin, thehighlyrepeatedgenesencodingthemajorribosomalRNAs(rRNAs)are loopedoutinstructurescallednucleoli.Thefibrillarcentresofthenucleoli arethesitesoftranscriptionofthesegenesandthetranscriptsareprocessed intheouterregionsofthenucleoli.
ThenucleusisboundedbythenuclearenvelopeorNE(Chapters2and3), whichconsists,ineffect,ofthreemembranouscomponents(showndiagrammaticallyinthecartooninFigure1.1).Firstly,theouterenvelopeisconnected
Cytoplasm
Rough ER continuous with outer nuclear envelope
Figure1.1 Diagrammaticcartoonofthenuclearenvelopeandnuclearpore complex.(FromEvans etal.,2004.)ReproducedbypermissionoftheSocietyfor ExperimentalBiology.
totheERandthelipidsandproteinsoftheouterNEaresimilartothose oftheroughER.Further,aswiththeroughER,ribosomesareoftenpresent ontheouterNE.So,theouterNEmaybeasiteofproteinsynthesisandis certainlyapartofthecell’sendomembranesystem.Secondly,thereisthe innerNEseparatedfromtheouterNEbythelumen,whichisabout30nm across.TheinnersurfaceoftheinnerNEiscloselyassociatedwiththenuclear lamina,astructureconsistingoffilamentousproteinsandwhichformsthe maincomponentofthenuclearmatrixornucleo-skeleton.Thirdlythereis theporemembrane,whichlinkstheinnerandouterNEsandformspartof thenuclearporecomplexorNPC(Chapters2,4and8).
Thecontainmentofchromatinwithinitsownmembrane-boundorganelle hasmajorimplicationsforthelifeofthecell.Amongstotherthings,itpermitspreciseandcomplexregulationofgeneactivityandDNAreplication ‘protected’frommoregeneralaspectsofcellularmetabolism.However,it alsoimposesconstraints.Thenucleusdoesnotcontainprotein-synthesizing machinery,eventhoughproteinsmaybemadeonthesurfaceoftheouter NE.Alltheenzymes,togetherwithstructuralandregulatoryproteinsnecessaryfortheactivitiesandcomponentsofthenucleus,over1000proteinsin all(NuclearProteinDatabase:http://npd.hgu.mrc.ac.uk/),mustbeableto getinfromtheoutside.Atthesametime,severalthousandmoreproteins, thosethatarenotinvolvedinthelifeofthenucleus,arekeptout.Thereare alsoproteinsthatshuttlebetweenthenucleusandthecytosol.Finally,all thedifferentRNAsthatfunctioninthecytosolmustleavethenucleus(in theformofnucleoproteincomplexes).TheNPCshaveamajorroleinthe
controlofentryintoandexitfromthenucleus(Chapters4and8),alongwith specificsignallingandtransportmechanisms.Thisprovidesonemorelevel ofregulationofchromatin-associatedbiochemicalactivity.
1.3Theplantnucleargenome
1.3.1Generalfeatures
ArecentreviewbyHeslop-HarrisonandSchwarzacher(2011)givesawealth ofinformationaboutplantnucleargenomes,whileChapters5and6inthis volumedealwithspecificaspectsofchromatinorganization.Inthischapter, thefocusisonthosefeaturesrelatedtogenomeevolutionandreplication. Higherplantgenomesvaryenormouslyinoverallsize,rangingoverthree ordersofmagnitude.Thereissomecorrelationbetweengenomesizeand nuclearsizesothat,ingeneral,plantswithlargegenomeshavelargernuclei thanplantswithsmallgenomes.Someofthedifferencesingenomesizehave arisenbyduplicationofindividualgenesandofwholegenomes(polyploidy). Withinindividualgenomes,muchoftheDNAdoesnotcodeforproteins orRNA.Comparisonbetweencloselyrelatedspecies(see,e.g.Bryantand Hughes,2011)thathavedifferingamountsofnuclearDNAshowthatmost ofthevariationcanbeaccountedforbyrepeatedDNAsequences.Someof thevariationisinthenumberofcopiesofrepeatedgenes,suchasthose codingforrRNAbutmostofitisaccountedforbyvariationsinnon-coding DNA.Thisincludeshighlyrepeated‘satellite’DNAofaround180basepairs perrepeat(Sibson etal.,1991;Round etal.,1997),simplesequencerepeats andretrotransposons.‘Satellite’DNAsequencesareconcentratedatthecentromereswheretheyappeartobeessentialforcentromerefunction(Nagaki etal.,2003andChapter6,thisvolume).Retrotransposonsorretro-elements includeLINES(longinterspersedsequences)andvarioushighlyrepetitive sequencesofdifferentsizesandcopynumber.Takentogethertheseretroelementscanmakeaverylargeproportionofthegenome(fordetails,see BryantandHughes,2011;Heslop-HarrisonandSchwarzacher,2011).There arealso‘fossil’codingsequencesorpseudogenes,someofwhichseemto havebeenderivedfromotherspecies.Allthesetypesofsequencearepresent tosomeextentinalleukaryotesandhavepossiblybeenfeaturesofchromatinsincethefirstappearanceoftheEukarya.However,overtheperiodin whichhigherplantshavebeenevolving,theirnucleargenomeshavebeen andcontinuetobeamongstthemostdynamic.
Asinalleukaryotes,theDNAitselfexistsaslinearmolecules,onelong doublehelixperchromosome.Inthechromosomes,theDNAiscomplexed withproteins,mainlythebasicproteinsknownashistones,toformchromatin,asdescribedinmoredetailinChapters5and6.Somechromatin (heterochromatin)remainscondensedandthereforeclearlyvisiblethroughoutthecellcycle.AsdescribedinmuchmoredetailinChapter6,muchofthe
heterochromatinislocatedatthecentromeres(andthusinvolves‘satellite’ DNA,mentionedabove)andatthetelomeres(endsofchromosomes).Bycontrastwithheterochromatin,themajorityofthechromatin,knownaseuchromatin,decondensesasmitosisiscompleted.Thesignificanceofthesetwo patternsofbehaviourandofthedistributionheterochromatinisdiscussedin Chapter6.
ThelinearstructureofeukaryoticDNAmoleculeshascausedsometo questiontheoriginsofeukaryoticgenomes(seeSection1.5).Theconsensus remainsthattheoriginalproto-eukaryotichostcellwasderivedfromthe archaeanlineageandyetamongstextantmembersoftheArchaea,wedo notyetknowofanythathavelinearchromosomes.Nevertheless,DNAin manyArchaeaiscomplexedwithhistone-likeproteinstoformfeaturesthat resemblethenucleosomesofeukaryoticchromatin(PereiraandReeve,1998; Sandman etal.,2001),albeitthatthesenucleosomescontainonly80basepairs ofDNAwrappedroundfour,noteighthistonemolecules(seeChapter5fora detaileddescriptionofeukaryoticchromatin)2 .Further,severaleubacteriaare knownthathavelinearchromosomes,andsomespeciesareabletomaintain bothlinearandcircularDNAmolecules(VolffandAltenbuchner,2000;Lin andMoret,2011),asituationthathasalsobeendescribedformitochondria insomelowerandhigherplantsandfungi(Borza etal.,2009;Lo etal.,2011). TheabsenceoflinearDNAmoleculesdoesnotthereforeruleoutArchaeaas beingprogenitorsoforasistergrouptotheproto-eukaryotes.
1.3.2Replicationofthenucleargenome
ThegeneralfeaturesofeukaryoticgenomesraiseseveralproblemsforDNA replication.Thesehavebeendiscussedmorefullyinanearlierpublication (Bryant,2010)butneedtobementionedbrieflyhere.Thefirstisthatthe complexofDNAandproteininchromatin(whichisofcoursecommonto alleukaryotes)meansthatcopyingtheDNAisslowerthaninprokaryotes. TakingthistogetherwiththelengthofeukaryoticDNAmolecules,especially insomeplantgenomes,hasledtotheevolutionofmultiplereplicationorigins (pointsatwhichreplicationmaystart)alongtheaxisofeachDNAmolecule. ThenatureofthesereplicationoriginsinrelationtoDNAstructurehasbeen amatterfordebateformanyyears(seee.g.Hern ´ andez etal.,1988;Van’t HofandLamm,1992;BryantandFrancis,2008;Bryant,2010;Lee etal.,2010; seealsoBerbenetz etal.,2010)anditisstillnotclearwhetherornotspecific sequencesareinvolved.Whatisclear,however,isthatoriginsareAT-richand arethereforemorepronetotransient,localizedshort-rangestrandseparation
2 Itmustalsobenotedthatmany,ifnotall,ArchaeapossessadifferenttypeofDNAbindingprotein,knownasAlba,whichisalsoabletogenerateaformofchromatinin whichtheDNAisinsidetheprotein(Tanaka etal.,2012)–i.e.verydifferentfromthe nucleosomestructure.
knownas‘breathing’.Itisalsoclearthatthetimingandorderinwhichthe originsareactiveensuresthattheDNAisreplicatedwithinanS-phasethat iscompletedwithinafewhours.ThereareagainlinkswiththeArchaeain thatseveralspecieshavemorethanonereplicationorigin(usuallytwoor three:LundgrenandBernander,2005;RobinsonandBell,2005),whichseem tobeattachedtospecificlocationsatthecell’speriphery(Gristwood etal., 2012).Likethereplicationoriginsofplants(andothereukaryotes),archaean originsareAT-richand,inthisgroup,specificsequenceisimportantfor correctfunction(MajernikandChong,2008).
Finally,theuni-directional(5 to3 )natureofDNAreplication,coupledwith theinabilityofDNApolymerasestoinitiatereplicationwithoutaprimer(see Bryant,2010)causesproblemsattheendsofmolecules.Thishasledtothe developmentduringevolutionofspecializedstructurescalledtelomeresat theendsofchromosomalDNAmolecules,withanassociatedenzyme,telomerase3 .AsdiscussedinChapter7,theendsareprotectedfromdegradation andfrombeinginappropriatelytargetedbytheDNArepairmachinery(see Chapter5)becauseofthetelomere/telomerasecombination.
Theenzymesandotherproteinswhichcarryoutreplicationofnuclear DNAinplantshavebeendescribedinsomedetailintworecentpapers (Schultz etal.,2007;Bryant,2010).Herethefocusisonaselectionofthose aspectsthatprovidecluesaboutevolution.Lookingfirstatpre-replication events(seee.g.Aves,2009;BryantandAves,2011),itisclearthatinplants,as inothereukaryotes,replicationoriginsareboundandtherefore‘marked’by acomplexofsixproteins,theOrigin-RecognitionComplex(ORC)(Collinge, etal.,2004;Mori etal.,2005;Shultz etal.,2007;Bryant2010).Aproteinknown asCDC6,alongwithCDT1,thenfacilitatestheloadingoftheCMGcomplexconsistingoftheGINShetero-tetramer,MCMs2-7(thehelicasethat separatesthetwostrandsofDNAatthereplicationfork)andtheprotein knownasCDC45,whichwilllaterfacilitateloadingoftheinitiatingDNA polymerase.LookingattheArchaea,itisclearthatbothrecognitionofreplicationoriginsandthefirststageintheiractivationarecarriedoutbya singleproteinthatisbothsimilartoandfulfilsthefunctionsoftheORC andCDC6(reviewedbyBryantandAves,2011).ThefunctionoftheGINS complexiscarriedouteitherbyahomo-tetramerortetramerconsistingof twodifferenthomo-dimers(Yoshimochi etal.,2008).Sequencesimilarityto eukaryoticGINSproteinsislimitedbuttheproteinsinteracttoformacomplexofsimilararchitecturetotheeukaryoticcomplex.WithrespecttoMCMs, mostArchaeahavejustone,whichformsahomohexamerascomparedwith theeukaryoticheterohexamer.HintsofmultipleMCMsareseenin Thermococcuskodakarensis (Pan etal.,2011),whichhasthree.BothMCMs2and3 canformhomohexamersbutonlyMCM3isessentialforDNAreplication.
3 SeealsothediscussiononlinearDNAmoleculesinmitochondria(e.g.Valach etal., 2011).
