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ANNUAL PLANT REVIEWS
VOLUME 35
Plant Systems Biology Edited by Gloria M. Coruzzi and Rodrigo A. Gutiérrez
© 2009 Blackwell Publishing Ltd. ISBN: 978-1-405-16283-8
i
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ANNUAL PLANT REVIEWS
VOLUME 35
Plant Systems Biology
Edited by
Gloria M. Coruzzi
DepartmentofBiologyandCenterforGenomicsandSystemsBiology
NewYorkUniversity, NewYork,NY, USA
Rodrigo A. Gutie´rrez
DepartmentofBiologyandCenterforGenomicsandSystemsBiology
NewYorkUniversity, NewYork,NY, USA
DepartamentodeGene´ticaMolecularyMicrobiolog´ıa
PontificiaUniversidadCato´licadeChile, Santiago,Chile
A John Wiley & Sons, Ltd., Publication
iii
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Thiseditionfirstpublished2009
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Annualplantreviews(Print) ISSN1460-1494
Annualplantreviews(Online) ISSN1756-9710
(cid:1)
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AnnualPlantReviews
Aseriesforresearchersandpostgraduatesintheplantsciences.Eachvolume
inthisseriesfocusesonathemeoftopicalimportanceandemphasisisplaced
onrapidpublication.
EditorialBoard:
Prof.JeremyA.Roberts(Editor-in-Chief),PlantScienceDivision,Schoolof
Biosciences,UniversityofNottingham,SuttonBoningtonCampus,
Loughborough,Leicestershire,LE125RD,UK;
DrDavidEvans,SchoolofBiologicalandMolecularSciences,Oxford
BrookesUniversity,Headington,Oxford,OX30BP;
Prof.HidemasaImaseki,Obata-Minami2419,Moriyama-ku,Nagoya463,
Japan;
DrMichaelT.McManus,InstituteofMolecularBioSciences,Massey
University,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.Laing,andA.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
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13. Plastids
EditedbyS.G.Moller
14. PlantPigmentsandtheirManipulation
EditedbyK.M.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
EditedbyDavidC.Logan
32. CellCycleControlandPlantDevelopment
EditedbyD.Inze´
33. IntracellularSignalinginPlants
EditedbyZ.Yang
34. MolecularAspectsofPlantDiseaseResistance
EditedbyJ.Parker
35. PlantSystemsBiology
EditedbyGloriaM.CoruzziandRodrigoA.Gutie´rrez
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CONTENTS
Contributors xi
Preface xiv
Acknowledgements xvi
PartI SystemsBiology:AnOverview
1 SystemsBiology:PrinciplesandApplicationsinPlantResearch 3
G.M.Coruzzi,A.Burga,M.S.KatariandR.A.Gutie´rrez
1.1 Introduction 4
1.2 Networkbiology 6
1.3 Experimentalapproachesforplantsystemsbiology 10
1.4 Strategiesforgenomicdataintegration 21
1.5 Systemsbiologyinplantresearch 26
1.6 Conclusion 31
2 AnOverviewofSystemsBiology 41
R.AlbertandS.M.Assmann
2.1 Systemstheoryandbiology 41
2.2 Graphelementsandnetworkattributes 42
2.3 Buildingbiologicalnetworks:identifyingnodesand
mappinginteractions 47
2.4 Buildingbiologicalnetworks:computationalmethods
fornetworkinference 52
2.5 Biologicalnetworkmodels:dataintegration 54
2.6 Biologicalnetworkmodels:fromnetwork
structuretodynamics 56
2.7 Perspectives 57
3 ProkaryoticSystemsBiology 67
T.Kacmarczyk,P.WaltmanandR.Bonneau
3.1 Introduction 67
3.2 Typesofquestions 68
3.3 Atypicalprokaryoticsystemsbiologyproject 70
3.4 Globalmodels 70
3.5 Comparativefunctionalgenomicsofprokaryotes 71
3.6 Reviewofcoretechnologiesforprokaryoticsystemsbiology 72
3.7 Caulobactercrescentus 77
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viii (cid:1) Contents
3.8 Bacillussubtilis 86
3.9 Escherichiacoli 95
3.10 HalobacteriumsalinariumNRC-1 109
3.11 Conclusion 122
4 AnimalSystemsBiology:TowardsaSystemsViewof
DevelopmentinC.Elegans 137
A.Fernandez,F.PianoandK.C.Gunsalus
4.1 WhyC.elegansasamodelfordevelopmental
systemsbiology? 138
4.2 Defininginvivofunctionsduringdevelopment:towards
aphenomemapofC.elegansembryogenesis 140
4.3 Dataintegration:towardsasystemsviewof
earlyembryogenesis 151
4.4 Conclusion 159
PartII PlantSystemsBiology:EnumeratingandIntegratingthe
SystemComponents
5 SoftwareToolsforSystemsBiology:VisualizingtheOutcomes
ofNExperimentsonMEntities 169
C.PoultneyandD.Shasha
5.1 Theworthwhilechallengeofinterdisciplinarywork 169
5.2 Sungeardesignprinciples 171
5.3 Combiningvisualizationtoolsforplantsystemsbiology 182
5.4 MapMan 183
5.5 Genevestigator 185
5.6 Cytoscape 187
5.7 VirtualPlant 189
5.8 Conclusion 192
6 ThePlantGenome:DecodingtheTranscriptionalHardwiring 196
E.GrotewoldandN.Springer
6.1 Introduction 196
6.2 Theplantbasaltranscriptionalapparatus 197
6.3 Planttranscriptionfactors 201
6.4 Hardwiringofregulatorysequences 207
6.5 Planttranscriptionalregulatorymotifs,modules
andnetworks 216
6.6 Conclusion 217
7 TheRNAWorld:IdentifyingmiRNA-TargetRNAPairsas
PossibleMissingLinksinMulti-NetworkModels 229
P.J.GreenandB.C.Meyers
7.1 Introduction 230
7.2 SequencingofsmallRNAs 232
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Contents (cid:1) ix
7.3 IdentificationofmiRNAs 233
7.4 IdentificationofmiRNAtargets 235
7.5 MicroRNA-targetmRNApairs:missinglinksin
multi-networkmodels? 236
8 Proteomics:SettingtheStageforSystemsBiology 243
S.C.Peck
8.1 Introduction:theneedforproteomicsinsystemsbiology 243
8.2 Determinationofproteinlocationinthecell 244
8.3 Identificationofdifferentproteinforms 246
8.4 Quantitation 248
8.5 Conclusion 254
9 Metabolomics:IntegratingtheMetabolomeandtheProteome
forSystemsBiology 258
W.Weckwerth
9.1 Themolecularhierarchyinbiochemicalnetworks,the
conceptofsystemsbiologyandfunctionalgenomicsin
thepost-genomeera 259
9.2 Metabolomicsandproteomics:post-genomedisciplines
intimatelyboundtomassspectrometrictechniques 261
9.3 Metabolomics:globalanalysisofrapidmetabolic
responsescombinedwithcomputer-aidediterative
metabolicmodelling 261
9.4 Applicationofmetabolomicsinmolecularplant
physiologyandbiochemistry 269
9.5 Measuringthekeyplayers:proteomics 273
9.6 Combiningmetabolomics,proteomicsandmultivariate
datamining:asystemsbiologyapproach 279
9.7 Conclusion 281
10 FromtheIonometotheGenome:IdentifyingtheGene
NetworksthatControltheMineralContentofPlants 290
M.L.Guerinot,I.BaxterandD.E.Salt
10.1 Introduction 290
10.2 Analyticalplatformsforionomics 291
10.3 Bioinformaticsplatformsforionomics 294
10.4 Arabidopsisasamodelsystemforionomics 295
10.5 Evolutionarycontextforionomics 298
11 DevelopmentandSystemsBiology:RidingtheGenomicsWave
TowardsaSystemsUnderstandingofRootDevelopment 304
S.M.BradyandP.N.Benfey
11.1 Rootsandsystemsbiology 304
11.2 Whystudyroots? 305
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x (cid:1) Contents
11.3 Rootdevelopmentinthemodelplant,Arabidopsisthaliana 305
11.4 Systemsbiologyatthemolecularlevel:modellingaroot
transcriptionalnetwork 308
11.5 Identificationofcomponents 309
11.6 Componentmodelling 314
11.7 Systemsbiologyatthecellularlevel:modellingroot
growthandthedynamicbehaviourofitscomponentcells 317
11.8 Systemsbiology:modellingtherootphysicalnetwork 323
11.9 Futuredirections 327
12 PerspectivesonEcologicalandEvolutionarySystemsBiology 331
C.L.Richards,Y.Hanzawa,M.S.Katari,I.M.Ehrenreich,
K.E.EngelmannandM.D.Purugganan
12.1 Emergentpropertiesofsystemsbiology,ecologyand
evolution 332
12.2 Complexenvironmentsandecologicalsystemsbiology 332
12.3 Genenetworksandtheecologicaltranscriptome 333
12.4 Analysisofsystemsbiologydata:theroleofecological
andevolutionarymethods 335
12.5 Theecologicalandevolutionarycontextofmodel
organisms:theexampleofArabidopsisandbeyond 336
12.6 Naturalvariationingenomesandgenenetworks 339
12.7 Thefutureofecologicalandevolutionarysystemsbiology 343
Index 351
Colorplate(betweenpages176and177)
