Plant Genes, Genomes and Genetics

261 Pages·2015·36.616 MB·English

by  Erich Grotewold, Joseph Chappell, Elizabeth A. Kellogg

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
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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
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CoverillustrationbyDebbieMaizels
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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