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Plant Genes, Genomes and Genetics Plant Genes, Genomes and Genetics Erich Grotewold The Ohio State University, USA Joseph Chappell University of Kentucky, USA Elizabeth A. Kellogg Donald Danforth Plant Science Center, St. Louis, Missouri, USA Thiseditionfirstpublished2015©2015byJohnWiley&Sons,Ltd Registeredoffice: JohnWiley&Sons,Ltd,TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK Editorialoffices: 9600GarsingtonRoad,Oxford,OX42DQ,UK TheAtrium,SouthernGate,Chichester,WestSussex,PO198SQ,UK 111RiverStreet,Hoboken,NJ07030-5774,USA Fordetailsofourglobaleditorialoffices,forcustomerservicesandforinformationabouthowtoapplyforpermissiontoreusethecopyright materialinthisbookpleaseseeourwebsiteatwww.wiley.com/wiley-blackwell. TherightoftheauthortobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewiththeUKCopyright,Designsand PatentsAct1988. 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LimitofLiability/DisclaimerofWarranty:Whilethepublisherandauthor(s)haveusedtheirbesteffortsinpreparingthisbook,theymake norepresentationsorwarrantieswithrespecttotheaccuracyorcompletenessofthecontentsofthisbookandspecificallydisclaimany impliedwarrantiesofmerchantabilityorfitnessforaparticularpurpose.Itissoldontheunderstandingthatthepublisherisnotengagedin renderingprofessionalservicesandneitherthepublishernortheauthorshallbeliablefordamagesarisingherefrom.Ifprofessionaladvice orotherexpertassistanceisrequired,theservicesofacompetentprofessionalshouldbesought. LibraryofCongressCataloging-in-PublicationData Grotewold,Erich,author. Plantgenes,genomes,andgenetics/ErichGrotewold,JosephChappell,ElizabethKellogg. pagescm Includesbibliographicalreferencesandindex. ISBN978-1-119-99888-4(cloth)–ISBN978-1-119-99887-7(pbk.)1.Plantmoleculargenetics.2.Plantgeneexpression. 3.Genomics.I.Chappell,Joseph,author.II.Kellogg,ElizabethAnne,author.III.Title. [DNLM:1.Plants–genetics.2.Genomics.3.PlantPhysiologicalPhenomena.4.RNA,Plant–genetics.QK981] QK981.4.G762015 572.8′2–dc23 2014028955 AcataloguerecordforthisbookisavailablefromtheBritishLibrary. Wileyalsopublishesitsbooksinavarietyofelectronicformats.Somecontentthatappearsinprintmaynotbeavailableinelectronicbooks. CoverillustrationbyDebbieMaizels Typesetin10/12ptMinionbyLaserwordsPrivateLimited,Chennai,India. 12015 Contents Acknowledgements xi Introduction xiii AbouttheCompanionWebsite xix PARTI: PLANTGENOMESANDGENES Chapter1 Plantgeneticmaterial 3 1.1 DNAisthegeneticmaterialofalllivingorganisms,includingplants 3 1.2 Theplantcellcontainsthreeindependentgenomes 8 1.3 AgeneisacompletesetofinstructionsforbuildinganRNAmolecule 10 1.4 Genesincludecodingsequencesandregulatorysequences 11 1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposableelementgenesareroughlythesame 12 1.6 GenomicDNAispackagedinchromosomes 15 1.7 Summary 15 1.8 Problems 15 References 16 Chapter2 Theshiftinggenomiclandscape 17 2.1 Thegenomesofindividualplantscandifferinmanyways 17 2.2 Differencesinsequencesbetweenplantsprovidecluesaboutgenefunction 20 2.3 SNPsandlengthmutationsinsimplesequencerepeatsareusefultoolsforgenome mappingandmarkerassistedselection 22 2.4 Genomesizeandchromosomenumberarevariable 28 2.5 SegmentsofDNAareoftenduplicatedandcanrecombine 30 2.6 Somegenesarecopiednearbyinthegenome 31 2.7 Wholegenomeduplicationsarecommoninplants 34 2.8 Wholegenomeduplicationhasmanyeffectsonthegenomeandongenefunction 37 2.9 Summary 41 2.10 Problems 42 Furtherreading 42 References 42 Chapter3 Transposableelements 45 3.1 Transposableelementsarecommoningenomesofallorganisms 45 3.2 Retrotransposonsaremainlyresponsibleforincreasesingenomesize 46 3.3 DNAtransposonscreatesmallmutationswhentheyinsertandexcise 52 3.4 Transposableelementsmovegenesandchangetheirregulation 57 3.5 Howaretransposableelementscontrolled? 60 v vi Contents 3.6 Summary 60 3.7 Problems 61 References 61 Chapter4 Chromatin,centromeresandtelomeres 63 4.1 Chromosomesaremadeupofchromatin,acomplexofDNAandprotein 63 4.2 Telomeresmakeuptheendsofchromosomes 66 4.3 Thechromosomemiddles–centromeres 71 4.4 Summary 77 4.5 Problems 77 Furtherreading 77 References 77 Chapter5 Genomesoforganelles 79 5.1 Plastidsandmitochondriaaredescendantsoffree-livingbacteria 79 5.2 Organellargeneshavebeentransferredtothenucleargenome 80 5.3 Organellargenessometimesincludeintrons 82 5.4 OrganellarmRNAisoftenedited 82 5.5 Mitochondrialgenomescontainfewergenesthanchloroplasts 84 5.6 Plantmitochondrialgenomesarelargeandundergofrequentrecombination 87 5.7 Allplastidgenomesinacellareidentical 91 5.8 Plastid genomes are similar among land plants but contain some structural rearrangements 93 5.9 Summary 95 5.10 Problems 95 Furtherreading 95 References 95 PARTII: TRANSCRIBINGPLANTGENES Chapter6 RNA 99 6.1 RNAlinkscomponentsoftheCentralDogma 99 6.2 StructureprovidesRNAwithuniqueproperties 102 6.3 RNAhasmultipleregulatoryactivities 105 6.4 Summary 108 6.5 Problems 108 References 109 Chapter7 TheplantRNApolymerases 111 7.1 TranscriptionmakesRNAfromDNA 111 7.2 VaryingnumbersofRNApolymerasesinthedifferentkingdoms 112 7.3 RNApolymeraseItranscribesrRNAs 114 7.4 RNApolymeraseIIIrecruitmenttoupstreamandinternalpromoters 116 7.5 Plant-specificRNP-IVandRNP-Vparticipateintranscriptionalgenesilencing 117 7.6 OrganelleshavetheirownsetofRNApolymerases 117 7.7 Summary 118 7.8 Problems 118 References 118 Contents vii Chapter8 MakingmRNAs–ControloftranscriptionbyRNApolymeraseII 121 8.1 RNApolymeraseIItranscribesprotein-codinggenes 121 8.2 ThestructureofRNApolymeraseIIrevealshowitfunctions 121 8.3 Thecorepromoter 123 8.4 Initiationoftranscription 125 8.5 Themediatorcomplex 127 8.6 Transcriptionelongation:theroleofRNP-IIphosphorylation 128 8.7 RNP-IIpausingandtermination 129 8.8 Transcriptionre-initiation 130 8.9 Summary 130 8.10 Problems 130 References 130 Chapter9 Transcriptionfactorsinterpretcis-regulatoryinformation 133 9.1 Informationonwhen,whereandhowmuchageneisexpressediscodifiedbythe gene’sregulatoryregions 133 9.2 Identifyingregulatoryregionsrequirestheuseofreportergenes 134 9.3 Generegulatoryregionshaveamodularstructure 135 9.4 Enhancers:Cis-regulatoryelementsormodulesthatfunctionatadistance 137 9.5 Transcriptionfactorsinterpretthegeneregulatorycode 138 9.6 Transcriptionfactorscanbeclassifiedinfamilies 138 9.7 HowtranscriptionfactorsbindDNA 139 9.8 Modularstructureoftranscriptionfactors 143 9.9 Organizationoftranscriptionfactorsintogeneregulatorygridsandnetworks 146 9.10 Summary 146 9.11 Problems 146 Morechallengingproblems 147 References 147 Chapter10 Controloftranscriptionfactoractivity 149 10.1 Transcriptionfactorphosphorylation 149 10.2 Protein–proteininteractions 151 10.3 Preventingtranscriptionfactorsfromaccesstothenucleus 155 10.4 Movementoftranscriptionfactorsbetweencells 156 10.5 Summary 158 10.6 Problems 158 References 158 Chapter11 SmallRNAs 161 11.1 Thephenomenonofcosuppressionorgenesilencing 161 11.2 DiscoveryofsmallRNAs 162 11.3 PathwaysformiRNAformationandfunction 163 11.4 PlantsiRNAsoriginatefromdifferenttypesofdouble-strandedRNAs 166 11.5 IntercellularandsystemicmovementofsmallRNAs 168 11.6 RoleofmiRNAsinplantphysiologyanddevelopment 170 11.7 Summary 171 11.8 Problems 171 References 172 viii Contents Chapter12 Chromatinandgeneexpression 173 12.1 PackinglongDNAmoleculesinasmallspace:thefunctionofchromatin 173 12.2 Heterochromatinandeuchromatin 173 12.3 Histonemodifications 174 12.4 Histonemodificationsaffectgeneexpression 175 12.5 Introducingandremovinghistonemarks:writersanderasers 175 12.6 ‘Readers’recognizehistonemodifications 177 12.7 Nucleosomepositioning 177 12.8 DNAmethylation 178 12.9 RNA-directedDNAmethylation 179 12.10 Controloffloweringbyhistonemodifications 180 12.11 Summary 181 12.12 Problems 181 References 181 PARTIII: FROMRNATOPROTEINS Chapter13 RNAprocessingandtransport 185 13.1 RNAprocessingcanbethoughtofassteps 185 13.2 RNAcappingprovidesadistinctive5’endtomRNAs 185 13.3 TranscriptionterminationconsistsofmRNA3’-endformationand polyadenylation 189 13.4 RNAsplicingisanothermajorsourceofgeneticvariation 192 13.5 ExportofmRNAfromthenucleusisagatewayforregulatingwhichmRNAs actuallygettranslated 194 13.6 Summary 196 13.7 Problems 196 References 196 Chapter14 FateofRNA 199 14.1 RegulationofRNAcontinuesuponexportfromnucleus 199 14.2 MechanismsforRNAturnover 199 14.3 RNAsurveillancemechanisms 201 14.4 RNAsorting 202 14.5 RNAmovement 203 14.6 Summary 204 14.7 Problems 204 Furtherreading 205 References 205 Chapter15 TranslationofRNA 207 15.1 Translation:akeyaspectofgeneexpression 207 15.2 Initiation 209 15.3 Elongation 209 15.4 Termination 210 15.5 Toolsforstudyingtheregulationoftranslation 211 15.6 Specifictranslationalcontrolmechanisms 211 Contents ix 15.7 Summary 213 15.8 Problems 214 Furtherreading 214 References 214 Chapter16 Proteinfoldingandtransport 215 16.1 Thepathwaytoaprotein’sfunctionisacomplicatedmatter 215 16.2 Proteinfoldingandassembly 215 16.3 Proteintargeting 218 16.4 Co-translationaltargeting 218 16.5 Post-translationaltargeting 219 16.6 Post-translationalmodificationsregulatingfunction 220 16.7 Summary 222 16.8 Problems 223 Furtherreading 223 References 224 Chapter17 Proteindegradation 225 17.1 Twosidesofgeneexpression–synthesisanddegradation 225 17.2 Autophagy,senescenceandprogrammedcelldeath 225 17.3 Protein-taggingmechanisms 226 17.4 Theubiquitinproteasomesystemrivalsgenetranscription 228 17.5 Summary 231 17.6 Problems 231 Furtherreading 231 Reference 231 Index 233