Plant transcription factors contribution in development metabolism and environmental stress vikas sr by lynn.cruz568

Transcription Factors:

Contribution in Development, Metabolism, and Environmental Stress

Vikas Srivastava

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ContributioninDevelopment, Metabolism,andEnvironmentalStress

PlantTranscriptionFactors

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PlantTranscriptionFactors

ContributioninDevelopment, Metabolism,andEnvironmentalStress

Editedby

VikasSrivastava

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu, Samba,JammuandKashmir(UT),India

SonalMishra

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu, Samba,JammuandKashmir(UT),India

ShaktiMehrotra

DepartmentofBiotechnology,InstituteofEngineeringandTechnology, Lucknow,UttarPradesh,India

SantoshKumarUpadhyay

DepartmentofBotany,PanjabUniversity,Chandigarh(UT),India

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Contents Listofcontributors............................................................................................................................xvii Abouttheeditors..............................................................................................................................xxiii Preface...............................................................................................................................................xxv SectionIPlanttranscriptionfactors(TFs)andgeneralaspects CHAPTER1Planttranscriptionfactors:anoverviewoftheirrolein plantlife ................................................................................................ 3 AksarAliChowdhary,SonalMishra,ShaktiMehrotra, SantoshKumarUpadhyay,DikshaBagalandVikasSrivastava 1.1 Introduction................................................................................................................3 1.2 Transcriptionfactorsandplantlife............................................................................4 1.3 Transcriptionfactorsandstressresponses.................................................................6 1.4 Transcriptionfactorsandsecondarymetabolism......................................................9 1.5 Conclusion................................................................................................................10 References.................................................................................................................11 CHAPTER2Adaptationofmilletstoaridland:aspecialperspective oftranscriptionfactors ....................................................................... 21 AlkaBishnoi,PoojaJangirandPraveenSoni Highlights..................................................................................................................21 Abbreviations............................................................................................................21 2.1 Introduction..............................................................................................................22 2.2 DistributionofaridlandinIndiaandworld...........................................................23 2.3 Millets:climate-smartnutri-cereals.........................................................................24 2.4 Stressasalimitingfactorforcropsinthearidzones.............................................27 2.5 Responsesofmilletstoabioticstresses...................................................................28 2.6 Transcriptionfactors:smartregulatorsofstresstoleranceinmillets.....................29 2.6.1WRKY..........................................................................................................30 2.6.2DOF..............................................................................................................31 2.6.3ERF/DREB...................................................................................................40 2.6.4NAC.............................................................................................................41 2.6.5bHLH............................................................................................................41 2.6.6ASR..............................................................................................................42 2.6.7bZIP..............................................................................................................42 2.6.8MYB.............................................................................................................42 2.6.9SBPs.............................................................................................................43 v

2.6.10Othertranscriptionfactors...........................................................................43 2.7 Harnessingthepotentialofmillettranscriptionfactors..........................................43 2.8 Conclusionandfutureperspectives.........................................................................46 Acknowledgments....................................................................................................47 Declarationofcompetinginterests..........................................................................47 Authorcontribution..................................................................................................47 References.................................................................................................................47 SectionIIPlantTFsanddevelopment .................................................. 61 CHAPTER3Planttranscriptionfactorsandrootdevelopment ............................. 63 RekhaChouhan,AbhilekKumarNautiyal, NancySharmaandSumitG.Gandhi 3.1 Introduction..............................................................................................................63 3.2 Plantrootarchitectureanddevelopment.................................................................64 3.3 Transcriptionfactorsinvolvedinplantrootdevelopment......................................64 3.3.1Rootapicalmeristem.....................................................................................64 3.3.2Lateralroots...................................................................................................67 3.3.3Roothair.........................................................................................................69 3.4 Conclusion................................................................................................................71 Acknowledgments....................................................................................................72 References.................................................................................................................72 CHAPTER4Therolesoftranscriptionfactorsinthedevelopmentof plantmeristems .................................................................................. 77 QingkunDongandCuiZhang 4.1 Introduction..............................................................................................................77 4.2 Shootapicalmeristem..............................................................................................77 4.3 Axillarymeristem.....................................................................................................79 4.4 Flowermeristem.......................................................................................................82 4.5 Intercalarymeristem.................................................................................................84 4.6 Conclusionandfutureperspectives.........................................................................84 Acknowledgments....................................................................................................88 Authorcontributions.................................................................................................88 References.................................................................................................................88 CHAPTER5Transcriptionfactorsandtheirroleinleafsenescence .................. 93 JeremyDkharandAsosiiPaul 5.1 Introduction..............................................................................................................93 vi Contents

5.2 Identificationoftranscriptionfactorfamiliesinsenescingleaf transcriptome............................................................................................................94

5.3 CharacterizationofleafsenescencerelatedTFsfamilies.......................................98

5.3.1Noapicalmeristem(NAM),ATAF1/2,CUP-shaped cotyledon2(CUC2)(NAC)TF...................................................................98

5.3.2WRKYTF..................................................................................................104

5.3.3APETALA2/Ethylene-responsiveelementbindingprotein (AP2/EREBP)superfamily........................................................................107

5.3.4Basichelix-loop-helix(bHLH)TFs..........................................................108

5.3.5MYBTFs...................................................................................................110

5.3.6AuxinresponsefactorandAuxin/INDOLE-3-aceticacidTFs.................110

5.3.7DNAbinding-with-one-finger(DOF)proteins.........................................112

5.3.8PSEUDO-responseregulatorsTF..............................................................113

5.3.9VQTFfamily.............................................................................................113

5.3.10Basicleucinezipper(bZIP)TFs................................................................113

5.3.11Homodomain-leucinezipper(HD-ZIP)TFs.............................................114

5.3.12PlantA/T-richsequenceandzinc-bindingprotein(PLATZ)TF.............115

5.3.13Growth-regulatingfactors(GRFS)andGRF-interacting factors(GIFS)............................................................................................115

5.3.14Teosintebranched1,Cycloidea,andproliferatingcellnuclear antigenbindingfactor(TCP)TFS.............................................................116

5.3.15Homeobox(HB)TFs.................................................................................116

5.3.16C3H(Zn)TFs.............................................................................................117

5.3.17GRASTFs..................................................................................................118

5.3.18CCAATbox-bindingTFs..........................................................................119

5.3.19HeatshockfactorTFs................................................................................119

5.3.20MADSTFs.................................................................................................119

5.3.21GOLDEN2,ARR-B,PSR1(GARP)familyTFs....................................120

5.3.22TRIHELIXTFs..........................................................................................120

5.3.23ArabidopsisresponseregulatorTFs..........................................................121

5.3.24Lateralorganboundaries/asymmetricleaves2.........................................122

5.3.25Earlyflowering3(ELF3)TF....................................................................122

5.3.26Ethyleneinsensitive3(EIN3)-like(EIL)TFS..........................................122

5.3.27Brinsensitive1(BRI1)-EMS-Suppressor1(BES1)TF.............................123

5.3.28Calmodulin-bindingtranscriptionactivator...............................................123

5.3.29TIFYTFs....................................................................................................124

5.3.30B-boxzincfingerTFs................................................................................124

5.4 Conclusion..............................................................................................................125

vii Contents

Acknowledgments..................................................................................................125 References...............................................................................................................126

CHAPTER6Planttranscriptionfactorsinlight-regulateddevelopment andUV-Bprotection.......................................................................... 139 DeekshaSingh,NevedhaRavindran,NikhilJob, PuthanValappilRahul,LavanyaBhagavatulaandSouravDatta 6.1 Introduction............................................................................................................139 6.1.1Transcriptionfactorsfamiliesinvolvedinlight-regulatedprocesses.........140 6.1.2Transcriptionfactorsassociatedwithvisiblelight-mediated developmentinplants..................................................................................143 6.1.3TranscriptionalregulationofUV-Bsignalinginplants.............................145 6.1.4Structuralandfunctionalevolutionoflight-responsiveplant transcriptionfactors.....................................................................................146 6.1.5Roleoflight-regulatedtranscriptionfactorsinothersignaling pathways.......................................................................................................148 6.2 Conclusion..............................................................................................................149 References...............................................................................................................149 CHAPTER7Tomatofruitdevelopmentthroughtheperspectiveof transcriptionfactors ......................................................................... 159 VigyasaSingh,DharitreePhukanandUjjalJyotiPhukan 7.1 Introduction............................................................................................................159 7.2 Transcriptionfactorsintomato..............................................................................160 7.3 MYBtranscriptionfactors.....................................................................................161 7.4 MADStranscriptionfactor.....................................................................................163 7.5 Othertranscriptionfactors.....................................................................................165 7.6 Conclusionandfutureperspectives.......................................................................166 Acknowledgment....................................................................................................167 Conflictofinterest..................................................................................................167 References...............................................................................................................167 CHAPTER8Planttranscriptionfactorsandnoduledevelopment ...................... 175 JawaharSinghandPraveenKumarVerma 8.1 Introduction............................................................................................................175 8.2 CCaMK/CYCLOPScomplex.................................................................................177 8.3 AP2-ERFtranscriptionfactor(ERN1andERN2)................................................179 8.4 GRAStranscriptionfactor.....................................................................................180 8.4.1Nodulationsignalingpathway1/2(NSP1andNSP2)................................180 8.5 SymSCL1...............................................................................................................181 8.6 NINandNIN-likeproteins....................................................................................181 8.7 StructureofNINandNLPs...................................................................................181 viii Contents

8.8 RegulationofNINforrhizobialinfectionintheepidermisbyCYCLOPS.........182 8.9 RegulationofNINbycytokinin-responseelementsforcell divisionsinthepericycle.......................................................................................182 8.10 NIN:amasterregulatorofnodulation..................................................................183 8.11 NIN asanegativeregulatorinsystemiccontrolofnodulation............................183 8.12 NINasapositiveregulatorinsystemiccontrolofnodulation.............................184 8.12.1Lob-domainprotein16...............................................................................185 8.12.2Nodulationpectatelyase1.........................................................................185 8.13 Rhizobium-directedpolargrowth..........................................................................186 8.14 NuclearfactorY.....................................................................................................186 8.14.1Shortinternodes/stylish..............................................................................187 8.15 Conclusionandfutureperspectives.......................................................................188 Acknowledgments..................................................................................................189 Declarationofcompetinginterest..........................................................................189 Contribution............................................................................................................189 References...............................................................................................................189 SectionIIIPlantTFsandmetabolism .................................................. 197 CHAPTER9Theregulatoryaspectsofplanttranscriptionfactorsin alkaloidsbiosynthesisandpathwaymodulation............................. 199 PravinPrakash,RiturajKumarandVikrantGupta Abbreviations..........................................................................................................199 9.1 Introduction............................................................................................................199 9.2 Planttranscriptionfactorfamiliesinvolvedinalkaloidbiosynthesis regulation................................................................................................................201 9.2.1APETALA2/ethyleneresponsefactor.........................................................201 9.2.2Basichelix-loop-helix..................................................................................205 9.2.3Basicleucinezipper.....................................................................................206 9.2.4Cys2/His2-type(transcriptionfactorIIIA-type)zinc-finger proteinfamily/Zinc-finger Catharanthus protein(ZCT)family.................207 9.2.5Myeloblastosis..............................................................................................207 9.2.6WRKY..........................................................................................................208 9.2.7Othertranscriptionfactors...........................................................................209 9.3 Transcriptionfactor-mediated modulationofalkaloidbiosynthesispathways...........209 9.3.1Overexpression.............................................................................................209 9.3.2Downregulation............................................................................................210 9.3.3CRISPR/Cas-mediatedgenomeediting.......................................................211 9.4 Conclusions............................................................................................................212 References...............................................................................................................212 ix Contents

CHAPTER10Planttranscriptionfactorsandflavonoidmetabolism .................... 219 RekhaChouhan,GarimaRaiandSumitG.Gandhi 10.1 Introduction............................................................................................................219 10.2 Plantflavonoids,majorsubclasses,andbiosynthesis...........................................220 10.3 Transcriptionfactorfamiliesassociatedwithplantflavonoidmetabolism..........221 10.3.1Roleofbasic-helix-loop-helixtranscriptionfactorsinplant flavonoidmetabolism.................................................................................222 10.3.2MYBtranscriptionfactorfamilyandplantflavonoidmetabolism..........224 10.3.3WD40transcriptionfactorsandplantflavonoidmetabolism...................225 10.3.4Roleofbasicleucine-zippertranscriptionfactorsinplant flavonoidmetabolism.................................................................................226 10.3.5RoleofWRKYtranscriptionfactorsinplantflavonoidmetabolism............227 10.4 Conclusions............................................................................................................227 Acknowledgments..................................................................................................227 References...............................................................................................................227 CHAPTER11Demystifyingtheroleoftranscriptionfactorsinplant terpenoidbiosynthesis...................................................................... 233 AjayKumar,ParulSharma,RakeshSrivastavaand PraveenChandraVerma 11.1 Introduction............................................................................................................233 11.2 Biosynthesisofterpenoids.....................................................................................234 11.2.1Biosynthesisofbasicterpenoidsprecursor(MVAandMEPpathway)........235 11.2.2Biosynthesisofisoprenoidintermediates..................................................235 11.2.3Biosynthesisofterpenesbyterpenesynthases..........................................237 11.3 Regulationofterpenoids........................................................................................239 11.3.1WRKY........................................................................................................241 11.3.2MYB...........................................................................................................241 11.3.3bHLH(basichelix loop helix)...............................................................242 11.3.4AP2/ERF....................................................................................................242 11.3.5bZIP............................................................................................................243 11.3.6SPL,YABBY,andotherTFs....................................................................244 11.4 Conclusion..............................................................................................................244 Acknowledgment....................................................................................................244 References...............................................................................................................244 CHAPTER12Theregulatorycircuitofironhomeostasisinrice: ataleoftranscriptionfactors .......................................................... 251 PoojaKanwarShekhawat,HasthiRamandPraveenSoni Highlights................................................................................................................251 x Contents

Abbreviations..........................................................................................................251 12.1 Introduction............................................................................................................252 12.2 Ironuptakeandtransport.......................................................................................253 12.3 Majortranscriptionfactorsinvolvedinironhomeostasis.....................................255 12.3.1RegulationofFedeficiency.......................................................................255 12.3.4RegulationofFetoxicity...........................................................................258 12.4 Regulationoftheregulators...................................................................................258 12.4.1Epigeneticregulation.................................................................................259 12.4.2Regulationatthetranscriptionallevel.......................................................259 12.4.3Regulationatthepost-transcriptionallevel...............................................259 12.4.4Regulationatthepost-translationallevel..................................................259 12.4.5Regulationbyplanthormones...................................................................260 12.5 Conclusionandfutureperspectives.......................................................................260 Acknowledgments..................................................................................................262 Authorcontribution................................................................................................262 References...............................................................................................................262 SectionIVPlantTFsandStress ........................................................... 269 CHAPTER13Impactoftranscriptionfactorsinplantabioticstress: arecentadvancementforcropimprovement 271 DivyaChauhan,DevendraSingh,HimanshuPandey,ZebaKhan, RakeshSrivastava,VinayKumarDhimanandVivekKumarDhiman 13.1 Introduction............................................................................................................271 13.2 Regulatoryfunctionoftranscriptionfactorsinresponsetoabioticstress............271 13.3 ABAsignalingpathway.........................................................................................272 13.4 JAsignalingpathway.............................................................................................274 13.5 Transcriptionfactorsinvolvedinabioticstresstolerance.....................................275 13.5.1MYBTFs...................................................................................................275 13.5.2NACTFs....................................................................................................275 13.5.3AP2/ERFTFs.............................................................................................276 13.5.4WRKYTFs................................................................................................277 13.6 Conclusion..............................................................................................................280 References...............................................................................................................280 CHAPTER14Planttranscriptionfactorsandtemperaturestress ........................ 287 TingtingZhangandYangZhou 14.1 Effectoftemperaturestressonplantgrowth........................................................287 14.1.1Effectofhigh-temperaturestressonplants...............................................287 xi Contents

14.1.2Effectoflow-temperaturestresstoplants.................................................288 14.2 Transcriptionfactorsinvolvedinresponsetotemperaturestress.........................289 14.2.1HSFtranscriptionfactor.............................................................................289 14.2.2MYBtranscriptionfactor...........................................................................290 14.2.3AP2/ERFtranscriptionfactors...................................................................291 14.2.4WRKYtranscriptionfactors......................................................................293 14.3 Conclusionsandperspectives................................................................................294 Acknowledgments..................................................................................................294 References...............................................................................................................294 CHAPTER15Planttranscriptionfactorsandosmoticstress ............................... 301 TingtingZhangandYangZhou 15.1 Effectsofosmoticstressonplantsanditsregulatorymechanism.......................301 15.1.1Stomatalclosure.........................................................................................301 15.1.2Osmoticregulationmechanism.................................................................302 15.1.3MechanismofROSgenerationandscavenging.......................................302 15.1.4ABAsignalingpathway.............................................................................303 15.2 Transcriptionfactorsareinvolvedinregulatingosmoticstress...........................304 15.2.1Osmoticstresscausedbysaltstress..........................................................304 15.2.2Osmoticstresscausedbydroughtstress...................................................305 15.2.3Osmoticstresscausedbylowtemperature...............................................305 15.3 Conclusionsandperspectives................................................................................306 Acknowledgments..................................................................................................307 References...............................................................................................................307 CHAPTER16Transcriptionalregulationofdroughtstressstimulus: challengesandpotentialforcropimprovement ............................. 313 GyanendraK.Rai,GayatriJamwal,IshaMagotra, GarimaRaiandR.K.Salgotra 16.1 Introduction............................................................................................................313 16.2 Regulatoryroleoftranscriptionfactorsindryspelltolerance.............................314 16.3 Transcriptionfactorandtheirmechanismsunderdroughtstress.........................316 16.3.1DNAbindingwithonefinger(DOF)........................................................316 16.3.2WRKYtranscriptionfactor........................................................................318 16.3.3Heatshockfactor.......................................................................................319 16.3.4NuclearFactor(NF-Ys).............................................................................320 16.3.5TCPtranscriptionfactorfamily.................................................................320 16.3.6AP2/ERBP..................................................................................................322 16.3.7AREB/ABFfamily.....................................................................................323 xii Contents

16.3.8NACtranscriptionfactors..........................................................................324 16.3.9MYB/MYCtranscriptionfactors...............................................................325 16.4 Conclusionandfutureprospects............................................................................327 References...............................................................................................................327 CHAPTER17Plantresponsetoheavymetalstress:aninsightintothe molecularmechanismoftranscriptionalregulation ....................... 337 MehaliMitra,PujaAgarwalandSujitRoy 17.1 Introduction............................................................................................................337 17.2 Toxiceffectsofheavymetalsinplants.................................................................340 17.3 Plantsignalinginresponsetoheavymetalstress.................................................341 17.4 MAPKsignalingunderheavymetalstress...........................................................343 17.5 Calcium calmodulinsignalingpathwayunderheavymetalstress.....................344 17.6 Hormonesignalinginresponsetoheavymetalstress..........................................345 17.7 Reactiveoxygenspeciesproductionanditsroleinheavymetalstress...............346 17.8 Roleoftranscriptionfactorsinheavymetalresistanceregulation.......................347 17.9 TheMYB-familytranscriptionfactorsunderHMstress......................................348 17.10 TheWRKY-familytranscriptionfactorsunderHMstress...................................352 17.11 ThebZIP-familytranscriptionfactorsunderHMstress.......................................353 17.12 TheAP2/ERF/DREB-familytranscriptionfactorsunderHMstress....................354 17.13 Conclusionandfutureperspectives.......................................................................355 Acknowledgments..................................................................................................355 References...............................................................................................................355 CHAPTER18Planttranscriptionfactorsandsaltstress ...................................... 369 TingtingZhangandYangZhou 18.1 Effectsofsaltstressonplants...............................................................................369 18.1.1Osmoticstress............................................................................................369 18.1.2Ionstress....................................................................................................369 18.1.3Oxidativestress..........................................................................................370 18.1.4Nutritionalstress........................................................................................370 18.2 Salttolerancemechanismsinplants......................................................................370 18.2.1Osmoticregulationmechanism.................................................................370 18.2.2Ionhomeostasismechanism......................................................................371 18.2.3Reactiveoxygenspeciesscavengingmechanism.....................................371 18.3 Transcriptionfactorsinvolvedinsaltstress..........................................................372 18.3.1bHLHtranscriptionfactors........................................................................372 18.3.2bZIPtranscriptionfactors..........................................................................373 18.3.3NACtranscriptionfactors..........................................................................373 xiii Contents

18.3.4WRKYtranscriptionfactors......................................................................374 18.3.5MYBtranscriptionfactors.........................................................................374 18.3.6Othertranscriptionfactorsparticipateinsaltstress..................................375 18.4 Conclusionsandperspectives................................................................................376 Acknowledgments..................................................................................................377 References...............................................................................................................377 CHAPTER19Planttranscriptionfactors:importantfactors controllingoxidativestressinplants .............................................. 383 ShikhaVerma,PankajKumarVermaandDebasisChakrabarty 19.1 Introduction............................................................................................................383 19.2 Oxidativestressandsources..................................................................................384 19.2.1ROSproduction..........................................................................................385 19.3 ROSscavenging.....................................................................................................396 19.4 Roleoftranscriptionfactorsintheregulationofstress-responsivegenes...........397 19.4.1AP2/ERFfamily.........................................................................................398 19.4.2ThebHLHfamily.......................................................................................399 19.4.3MYBfamily...............................................................................................399 19.4.4TheNACfamily........................................................................................400 19.4.5TheWRKYfamily.....................................................................................400 19.4.6ThebZIPfamily.........................................................................................401 19.4.7TheHSFfamily.........................................................................................401 19.5 Conclusionandfutureprospects............................................................................402 Acknowledgments..................................................................................................403 References...............................................................................................................403 Furtherreading.......................................................................................................417 CHAPTER20Transcriptionfactors:masterregulatorsofdisease resistanceincropplants .................................................................. 419 RaviRanjanSaxesena,ShreenivasKumarSinghand PraveenKumarVerma 20.1 Introduction............................................................................................................419 20.2 Molecularbasisofplant microbeinteraction......................................................420 20.3 TheWRKYfamilyoftranscriptionfactorsandtheirfunctionaldomain............422 20.4 WRKYtranscriptionfactorsandtheirroleinbioticstress...................................423 20.5 APETELA2/ethylene-responsivefactorfamilyoftranscriptionfactors...............427 20.6 AP2/ERFfamilyoftranscriptionfactorsandtheirroleinbioticstress...............428 20.7 NACtranscriptionfactorsandtheirstructuralorganization.................................429 20.8 NACtranscriptionfactorsandtheirroleinbioticstress......................................430 xiv Contents

20.9 bZIPtranscriptionfactors.......................................................................................433 20.10 bZIPtranscriptionfactorsandtheirroleinbioticstress.......................................433 20.11 MYBtranscriptionfactorfamily...........................................................................434 20.12 MYBtranscriptionfactorsandtheirroleinbioticstress......................................435 20.13 Conclusionandfutureperspectives.......................................................................435 Acknowledgments..................................................................................................436 Declarationofcompetinginterest..........................................................................436 Contribution............................................................................................................436 References...............................................................................................................436 Index..................................................................................................................................................445 xv Contents

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Listofcontributors

PujaAgarwal

DepartmentofBotany,ConstituentCollege,PurneaUniversity,Purnia,Bihar,India

DikshaBagal

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu,Samba,Jammu andKashmir(UT),India

LavanyaBhagavatula

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

AlkaBishnoi

DepartmentofBotany,UniversityofRajasthan,Jaipur,Rajasthan,India

DebasisChakrabarty

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India

DivyaChauhan

DivisionofGermplasm,ICAR-NationalBureauofPlantGeneticResources,NewDelhi,Delhi, India

RekhaChouhan

CSIR-IndianInstituteofIntegrativeMedicine,Jammu,JammuandKashmir,India;GuruNanak DevUniversity(GNDU),Amritsar,Punjab,India

AksarAliChowdhary

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu,Samba,Jammu andKashmir(UT),India

SouravDatta

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

VinayKumarDhiman

DepartmentofBasicSciences,Dr.YSPUHFNauni,Solan,HimachalPradesh,India

VivekKumarDhiman

DepartmntofBiotechnology,HimachalPrade shUniversity,Shimla,HimachalPradesh, India

JeremyDkhar

PlantEvoDevoLaboratory,AgrotechnologyDivision,CSIR-InstituteofHimalayanBioresource Technology,Palampur,HimachalPradesh,India;AcademyofScientificandInnovative Research(AcSIR),Ghaziabad,UttarPradesh,India

QingkunDong

KeyLaboratoryofPlantMolecularPhysiology,CASCenterforExcellenceinMolecularPlant Sciences,InstituteofBotany,ChineseAcademyofSciences,Beijing,P.R.China

xvii

SumitG.Gandhi

CSIR-IndianInstituteofIntegrativeMedicine,Jammu,JammuandKashmir,India;Academyof ScientificandInnovativeResearch(AcSIR),Ghaziabad,UttarPradesh,India

VikrantGupta

PlantBiotechnologyDivision,CSIR-CentralInstituteofMedicinalandAromaticPlants (CSIR-CIMAP),Lucknow,UttarPradesh,India;AcademyofScientificandInnovativeResearch (AcSIR),CSIR-HRDCCampus,Ghaziabad,UttarPradesh,India

GayatriJamwal

SchoolofBiotechnology,S.K.UniversityofAgriculturalSciences&TechnologyofJammu, Chatha,JammuandKashmir,India

PoojaJangir

DepartmentofBotany,UniversityofRajasthan,Jaipur,Rajasthan,India

NikhilJob

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

ZebaKhan

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India

AjayKumar

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India

RiturajKumar

IshaMagotra

SchoolofBiotechnology,S.K.UniversityofAgriculturalSciences&TechnologyofJammu, Chatha,JammuandKashmir,India

ShaktiMehrotra

DepartmentofBiotechnology,InstituteofEngineeringandTechnology,Lucknow,UttarPradesh, India

SonalMishra

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu,Samba,Jammu andKashmir(UT),India

MehaliMitra

DepartmentofBotany,UGCCentreforAdvancedStudies,TheUniversityofBurdwan,Golapbag campus,Burdwan,WestBengal,India

AbhilekKumarNautiyal

CSIR-IndianInstituteofIntegrativeMedicine,Jammu,JammuandKashmir,India;Academyof ScientificandInnovativeResearch(AcSIR),Ghaziabad,UttarPradesh,India

xviii Listofcontributors

HimanshuPandey

DepartmentofBiotechnology,Dr.YSPUHFNauni,Solan,HimachalPradesh,India

AsosiiPaul

DepartmentofBotany,NagalandUniversity,Lumami,Nagaland,India

DharitreePhukan

ICAR-NationalInstituteforPlantBiotechnology,NewDelhi,Delhi,India

UjjalJyotiPhukan

SchoolofPlantSciences,UniversityofArizona,Tucson,AZ,UnitedStates

PravinPrakash

PlantBiotechnologyDivision,CSIR-CentralInstituteofMedicinalandAromaticPlants(CSIR-CIMAP), Lucknow,UttarPradesh,India

PuthanValappilRahul

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

GarimaRai

CSIR-IndianInstituteofIntegrativeMedicine,Jammu,JammuandKashmir,India

GyanendraK.Rai

SchoolofBiotechnology,S.K.UniversityofAgriculturalSciences&TechnologyofJammu, Chatha,JammuandKashmir,India

HasthiRam

NationalInstituteofPlantGenomeResearch,NewDelhi,Delhi,India

NevedhaRavindran

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

SujitRoy

DepartmentofBotany,UGCCentreforAdvancedStudies,TheUniversityofBurdwan,Golapbag campus,Burdwan,WestBengal,India

R.K.Salgotra

SchoolofBiotechnology,S.K.UniversityofAgriculturalSciences&TechnologyofJammu, Chatha,JammuandKashmir,India

RaviRanjanSaxesena

PlantImmunityLaboratory,NationalInstituteofPlantGenomeResearchArunaAsafAliMarg, NewDelhi,Delhi,India

NancySharma

CSIR-IndianInstituteofIntegrativeMedicine,Jammu,JammuandKashmir,India

ParulSharma

BiologicalCentralFacility,CSIR-CentralInstituteofMedicinalandAromaticPlants,Lucknow, UttarPradesh,India

xix Listofcontributors

xx Listofcontributors

PoojaKanwarShekhawat

DepartmentofBotany,UniversityofRajasthan,Jaipur,Rajasthan,India

DeekshaSingh

PlantCellandDevelopmentalBiologyLaboratory,DepartmentofBiologicalSciences,IISER Bhopal,Bhauri,MadhyaPradesh,India

DevendraSingh

DepartmentofBiotechnology,B.N.CollegeofEngineeringandTechnology,Lucknow,Uttar Pradesh,India

JawaharSingh

PlantImmunityLaboratory,NationalInstituteofPlantGenomeResearch,ArunaAsafAliMarg, NewDelhi,Delhi,India

ShreenivasKumarSingh

PlantImmunityLaboratory,NationalInstituteofPlantGenomeResearchArunaAsafAliMarg, NewDelhi,Delhi,India

VigyasaSingh

PharmacologyandToxicologyDepartment,CollegeofPharmacy,UniversityofArizona,Tucson, AZ,UnitedStates

PraveenSoni

DepartmentofBotany,UniversityofRajasthan,Jaipur,Rajasthan,India

RakeshSrivastava

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India

VikasSrivastava

DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu,Samba,Jammu andKashmir(UT),India

SantoshKumarUpadhyay

DepartmentofBotany,PanjabUniversity,Chandigarh(UT),India

PankajKumarVerma

DepartmentofBotany,UniversityofLucknow,Lucknow,UttarPradesh,India;French AssociatesInstituteforAgricultureandBiotechnologyofDrylands,JacobBlausteinInstitutesfor DesertResearch,Ben-GurionUniversityoftheNegev,Israel

PraveenChandraVerma

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India

PraveenKumarVerma

PlantImmunityLaboratory,SchoolofLifeSciences,JawaharlalNehruUniversity,NewDelhi, Delhi,India

ShikhaVerma

MolecularBiologyandBiotechnologyDivision,CSIR-NationalBotanicalResearchInstitute, Lucknow,UttarPradesh,India;FrenchAssociatesInstituteforAgricultureandBiotechnology ofDrylands,JacobBlausteinInstitutesforDesertResearch,Ben-GurionUniversityofthe Negev,Israel

CuiZhang

KeyLaboratoryofPlantMolecularPhysiology,CASCenterforExcellenceinMolecularPlant Sciences,InstituteofBotany,ChineseAcademyofSciences,Beijing,P.R.China;CollegeofLife Sciences,UniversityofChineseAcademyofSciences,Beijing,P.R.China

TingtingZhang

SchoolofHorticulture,HainanUniversity/KeyLaboratoryforQualityRegulationofTropical HorticulturalCropsofHainanProvince,Haikou,P.R.China

YangZhou

SchoolofHorticulture,HainanUniversity/KeyLaboratoryforQualityRegulationofTropical HorticulturalCropsofHainanProvince,Haikou,P.R.China

xxi Listofcontributors

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Abouttheeditors

Dr.VikasSrivastava worksasanassistantprofessorintheDepartmentof Botany,attheCentralUniversityofJammuinIndiaandcurrentlyworking as‘RoyalSociety-NewtonInternationalFellow’atJohnInnesCentre, Norwich,UnitedKingdom.HecompletedhisPhDjointlyfromtheCentral InstituteofMedicinalandAromaticPlants(CSIR-CIMAP)andLucknow University,India.Furthermore,hepursuedapostdocattheNational InstituteofPlantGenomeResearch(NIPGR)inNewDelhi,India.With specializationsinvariousaspectsofbiotechnology,hehasacquiredthe trainingandexperiencetocarryoutresearchindiversefieldsofplantbiology.Hehaspublishedmanyarticlesinjournalsandbooksofinternational reputeandworkedasaprincipalinvestigatorforamajorprojectsanctionedbyUniversityGrantCommission(UGC)inNewDelhi.Heisarecipientofvariousawards andprestigiousfellowships.Hedeliveredseveralinvitedlecturesforinstitutesofnationalrepute.

Dr.SonalMishra workedasguestfacultyintheDepartmentofBotanyat theCentralUniversityofJammuinIndia.ShepursuedherPhDjointlyfrom CSIR-CIMAPinLucknowandJawaharlalNehruUniversityinNewDelhi. Previously,shecompletedherpostdocastheDr.D.S.Kothari-PostDoctoral Fellow(UGC-DSKPDF)andSERB-NationalPostdocFellow(SERB-NPDF) attheSchoolofBiotechnology,UniversityofJammuinIndia.Shealso gainedpostdocexperienceatJawaharlalNehruUniversityandNIPGR,in NewDelhi,India.Withspecializations invariousaspectsofbiotechnology, shehasacquiredthetrainingandexperiencetocarryoutresearchindiverse fieldsofplantbiotechnologyandmolecularbiology.Shehaspublishedmany articlesinjournalsandbooksofinternationalreputeandhasreceivedvarious awardsandprestigiousfellowships.Shehaspresentedherworkinseveral seminarsandconferencesandreceivedappreciation.

Dr.ShaktiMehrotra isaconsultingscientistintheDepartmentof BiotechnologyattheInstituteofEngineeringandTechnology,Dr.A.P.J. AbdulKalamTechnicalUniversityinLucknow,India.Shecompletedher PhDjointlyfromCSIR-CIMAPandLucknowUniversity,India. Furthermore,shepursuedherpostdocattheInstituteofEngineeringand Technology,Lucknow(DBT-PDF)andCSIR-CIMAP(DSTYoung Scientist).Withspecializationsinvariousaspectsofbiotechnology,she hasacquiredthetrainingandexperiencetocarryoutresearchinthe diversefieldsofplantbiotechnology.Atpresent,sheisworkinginthearea of3Dbioprintingand3Dfoodprinting.Shehaspublishedmanyarticlesin journalsandbooksofnationalandinternationalreputeandworkedasa principalinvestigatorformajorprojectssanctionedbytheDepartmentof

xxiii

ScienceandTechnology(DST)andDepartmentofBiotechnology(DBT),GovernmentofIndia. Sheisarecipientofvariousawardsandprestigiousfellowships.Shehasdeliveredseveralpresentationsatconferencesandworkshopsandhasreceivedappreciation.

Dr.SantoshKumarUpadhyay currentlyworksasanassistantprofessor intheDepartmentofBotanyatPanjabUniversityinChandigarh,India. Earlier,hewasDST-INSPIREfacultyattheNationalAgri-Food BiotechnologyInstitute,DepartmentofBiotechnology,Governmentof IndiainMohali,Punjab,India.Hecompletedhisdoctoralworkatthe CSIR-NationalBotanicalResearchInstitute,Lucknow,andwasawarded hisPhDinbiotechnologyfromUPTechnicalUniversity,inLucknow, India.Hehasbeenworkinginplantbiotechnologyformorethan15years andcurrentlyworksintheareaoffunctionalgenomics.Duringhisdoctoral research,hewasinvolvedinthecharacterizationofvariousinsecttoxic proteinssuchaslectins,chitin-bindingproteins,andothersfromplantbiodiversity.Currently,hisresearchgroupatPUhascharacterizednumerousimportantcationtransporters,includingcalciumcationantiporters,monovalentcationtransporters,calciumATPases,and importantdefense-relatedproteinfamiliessuchasreceptor-likekinases,antioxidantenzymes,of breadwheat.TheyalsocharacterizelongnoncodingRNAsrelatedtotheabioticandbioticstress response.Hehasalsodemonstratedthemethodofgenomeeditinginbreadwheatusingthe CRISPR-CassystemforfunctionalgenomicsstudiesandhasdevelopedatoolSinderforCRISPR targetsiteprediction.Hehasauthoredmorethan100publications,includingresearchpapersin leadingjournalsofinternationalrepute,nationalandinternationalpatents,bookchapters,and books.Inrecognitionofhisstrongcredentialsandcontributions,hehasbeenawardedtheNAAS Youngscientistaward(2017 18)andNAAS-Associate(2018)fromtheNationalAcademyof AgriculturalSciences,India,INSAMedalforYoungScientist(2013)fromtheIndianNational ScienceAcademy,India,NASI-YoungScientistPlatinumJubileeAward(2012)fromtheNational AcademyofSciences,India,andAltechYoungScientistAward(2011).HehasalsobeentherecipientoftheprestigiousDST-INSPIREFacultyFellowship(2012),SERB-EarlyCareerResearch Award(2016)fromtheMinistryofScienceandTechnology,GovernmentofIndia,SBS-MKU GenomicsAward(2019)fromtheBiotechResearchSocietyofIndia,andseveralresearchgrants fromvariousfundingagencieslikeSERB,DBT,andCSIR.Dr.Upadhyayalsoservesasamember oftheeditorialboardandareviewerofmanypeer-reviewedinternationaljournals.

xxiv Abouttheeditors

Preface

Transcriptionfactors(TFs)arevitalproteinmoleculesinvolvedinbiologicalprocessessuchas growth,development,andtheorganism’sresponsetoenvironmentalvariables.TheseproteinmoleculesbindtoDNAregulatorysequencesandregulatetheuniqueexpressionofeachgeneindifferentcelltypesandduringdifferentdevelopmentalphases.AnalysisandunderstandingofTF expressionandactivitiescanhelpresearchersestablishthesignificanceoftheirrolesinvariousbiologicalprocesses.ScientificexplorationandunderstandingofTFsandtheirgeneregulationisone ofthemostdynamicfieldsofresearchandtechnicaladvancements,givingawidescopetocompile whatisknown,whatisnotknown,andhowtheknownfactscanbeharnessedforfutureresearch. Theprincipalaimofthebook PlantTranscriptionFactors:ContributioninDevelopment, Metabolism,andEnvironmentalStress istoprovidearesourcecomprisingsignificantfacetsofTFs inplantbiology.

Thebookintendstoprovideamethodologicalreservehighlightingseveralstirringadvancementsthatmaystrengthenandexpandthereader’sknowledgebaseofthecomplexityoftranscriptionalcontrolsofbiologicalprocesses.Thebookcomprisesfoursectionsandincludeschaptersthat focusontherecentscientificexplorationsongeneralaspectsofplantTFsandtheircontributionto plantdevelopment,metabolicprocesses,andstressmanagement.Thechapterscompileexistingkey conceptsaswellasadvancedinformationimportantforbetterinsightintoTFtargetingandspecificity,thepropertiesofregulatorysequence,andmechanismsofTFaction,andpresentaplantTF informationrepertoire.Thetopicsselectedarediversefromthoseincludedinothermethodologicallyorientedbooksontranscriptionalregulationofplantbiologicalprocesses.

SectionI ofthebookincludestwochapters(Chapters1and2)thatcompriseacomprehensive overviewofTFsandtheirroleinplantlife. Chapter1 givesgeneral,yetupdatedinformationon thetypesofplantTFs. Chapter2 discussestheroleofplantTFsintheadaptionofmilletinarid lands.

SectionII encompasses Chapters3 8,whichfocusontranscriptionalregulationonplantdevelopmentinorganogenesis(root,meristem,leaves,fruit,andnoduledevelopment)andlight-regulated developments.Thissectionprovidescurrentknowledgeonthebiologicalfunctionsperformedby variousplantTFsandexplorestheexistingmoleculardatatoillustratehowtheyexerttheirroles duringplantdevelopment.

SectionIII consistsoffourchapters(Chapters9 12)thatcomprehensivelydiscussplantTFs associatedwithbiochemicalchanges(biosynthesisandregulationofsecondarymetabolitessuchas alkaloids,flavonoids,andterpenes)andbiochemicaldevelopments(suchasironhomeostasis).This sectionshedslightontranscriptionalregulationofvariousbiosyntheticpathwaygenesandsignalingcascadestoperformhighlyorchestratedbiologicalfunctionsatthemolecularlevel.

SectionIV (Chapters13 20)focusesonplantTFsassociatedwithstressmanagementandmitigationthatsubsequentlyleadstostresstoleranceandsurvivalofplants.Stress,bothbioticandabiotic,causesseveredamagetoallplants;however,theextentofdamagedependsuponthegrowth stageanddevelopmentalphaseofplants.Chaptersinthissectioncovercriticaldiscussionsand cross-talksonmolecularregulatorystrategiesofplants,withparticularreferencetocropstomaintainvitalphysiologicalactivitiesfortheirsurvivalundervariousbioticandabioticstressesduring specificgrowthstagesanddevelopmentalphases.

xxv

Weexpressourgratitudetoalltheauthorsfortheiroutstandingandcutting-edgecontributions tothebook.Insomeinstances,thisbookrepresentsthemostcurrentinsights,scientificopinions, andperspectivesintothetranscriptionalregulationofvariousplantprocesses,underscoringthe authors’generosityinsharingtheirveryrecentscientificprogressinabench-sidereferenceformat.

Wewouldalsoliketotakethisopportunitytoacknowledgethereviewersof PlantTranscription Factors:ContributioninDevelopment,Metabolism,andEnvironmentalStress fortheirgenerous helpandsuggestionswhilereviewingchaptermanuscripts.Wehopethisbookisatimelycontributionthatwillserveasaninformationreserveforthecurrentandnextgenerationofacademicians andscientistsworkingtodecipherthemysteriesofplantbiologybystudyingtheintricatenatureof transcriptionalregulation.

VikasSrivastava

SonalMishra

ShaktiMehrotra

SantoshKumarUpadhyay

xxvi Preface

Planttranscription factors(TFs)and generalaspects

SECTION I

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Planttranscriptionfactors:an overviewoftheirroleinplantlife

AksarAliChowdhary1,SonalMishra1,ShaktiMehrotra2,SantoshKumarUpadhyay3, DikshaBagal1 andVikasSrivastava1

1DepartmentofBotany,SchoolofLifeSciences,CentralUniversityofJammu,Samba,JammuandKashmir(UT), India 2DepartmentofBiotechnology,InstituteofEngineeringandTechnology,Lucknow,UttarPradesh,India 3DepartmentofBotany,PanjabUniversity,Chandigarh(UT),India

1.1 Introduction

Transcriptionfactors(TFs)arethemasterregulatorofgeneexpressionandaremainlyassociated withplantdevelopment,metabolism,andstressmanagement( Yangetal.,2012;Mishraetal., 2013;SrivastavaandVerma,2015;Srivas tavaetal.,2017;Bailloetal.,2019 ).TFsperformgene regulatoryactivitiesbyb indingtolocalordistal cis -elements(commonlyknownas DNA-bindingsites)ofgenesassociatedwithvariousbiologicalfunc tions.OnceaTFbindson theDNAbindingsiteofaparticularDNAsequence,itbringsouttheactivationorrepression activitythroughitsactivatororrepressordomains,respectively.TFsmayalsohaveotherdomains thatinteractwithotherproteins, suchasotherTFs,signalingmolecules,etc.,whichaddstotheir functionaldiversity(PhillipsandHoopes,2008).Forinstance,theposttranslationalmodification (phosphorylation)ofseveralTFshasbeena ssociatedwiththeMAPKcascadesystem( Guan etal.,2014).ThoughTFsareconsideredthecentralregulatorsofthebiologicalfunctionsofplant life,theyarealsoregulatedsignificantly underdiverseinternalandexternalstimuli(Srivastava andVerma,2015;Kumaretal.,2016).Further,manyplantTFsareknowntoregulatemultiple functions.Forinstance,thesignificanceofWRKYandAP2arereportedinstresstoleranceand theregulationofplant-specificmetabolism( Mishraetal.,2013,2015;Kumaretal.,2016).AsignificantportionoftheplantgenomeencodesforTFs,asreportedinthecaseofArabidopsis, where . 5%ofthegenesinthegenomeencodesTFs(ArabidopsisGenomeProject; Riechmann andRatcliffe,2000). Hawkinsetal.(2021) generatedthegenome-scalemetabolicpathwaydatabasesof126algalandplantgenomes,includingmodelcropsandmedicinalplants,considering thesignificanceofTFs.Duetothepivotalrole ofTFsintheregulationofseveralmolecular eventsofplantbiology,understandingtheirfunctionaldiversityisimmenselyimportantandrelevantforexploringthemolecularbiologyofplants.Therefore,thisbookexploresplantTFsand theirfunctionalpotentialandsignificance includingupdatedscientificresearchonTFs.

CHAPTER

1.2 Transcriptionfactorsandplantlife

Severalexternalandinternalsignalsgovernplant’sdevelopmentaldecisions.TFsparticipatein majorregulatoryprocessesthatareimportantforplant’sgrowth,development,andsurvival.TFs providestrictregulationatthetranscriptionallevelbymodulatingtheexpressionofmajorregulatorypathwaygenes. Table1.1 listssomeexamplesofplantTFsinvolvedinregulatingdifferent developmentaleventsofplantlife.

Inplantlife,seedgerminationistheinitialdevelopmentalstagestrictlyregulatedatthemolecularlevel.Inadditiontodormancy-relatedfactorsandplanthormones,theTFsactivelyregulate seedgerminationinplantsatthemolecularlevel.SomeimportantTFsthatcontrolseedgerminationincludebZIP44(Iglesias-Fern ´ andezetal.,2013),MADS-boxTFAGL21(Yuetal.,2017), NF-YCTF(Liuetal.,2016),andDOF(DNA-bindingwithonefinger, Rutaetal.,2020). Moreover,aB3-domainTF,FUSCA3(FUS3),andaGATA-typezincfingerfamilyTF,GATA12, in Arabidopsisthaliana controlprimaryseeddormancy(Chiuetal.,2012;Ravindranetal.,2017). Further,theinvolvementoftwobasichelix-loop-helix(bHLH)TFsTCP14andTCP15intheregulationofgibberellicacid(GA)-mediatedseedgerminationisalsoreported(Xuetal.,2020).These TFsinteractwith EXPANSIN (EXPA)genepromoterandregulatehormonebiosynthesis.

Table1.1Transcriptionfactorsidentifiedfortheirroleinplantdevelopment.

PlantsystemTranscriptionfactorsFunctionReferences

Arabidopsisthaliana

A.thaliana

Brassicarapa

Glycinemax

Oryzasativa

AtWRKY75Overexpressionin A.thaliana acceleratesflowering

AtTCPExpressionin A.thaliana promotedLeafdevelopment

AtAP2/ERF2(DRNL)Expressionin A.thaliana promotedgynoecium development

AtGISExpressionin Nicotianatabacum regulatesthedevelopmentof glandulartrichomes

AtWOX11/12Expressionin A.thaliana initiatesrootprimordia/root organogenesis

AtLBD29Expressionin A.thaliana promotedlateralrootemergence

BrZFP38Expressionin B.rapa promoted flowerdevelopment

L.GmNAC004Overexpressionin A.thaliana promotedlateralroot development

OsTCL1Expressionin A.thaliana inducesroothairdevelopment

Zhangetal.(2018b)

Koyamaetal.(2017)

Dur ´ an-Medinaetal. (2017)

Liuetal.(2017)

HuandXu(2016)

Porcoetal.(2016)

Lyuetal.(2020)

Quachetal.(2014)

Zhengetal.(2016)

Solanumlycopersicum

L.SlWUSExpressionin S.lycopersicum assistsflowerdevelopment

Lietal.(2017)

4Chapter1 Planttranscriptionfactors:anoverviewoftheirroleinplantlife

Furthermore,thesignificanceofTFsinimprovingseedgerminationunderstressconditionsisalso reported.Forinstance,OsbHLH035TFisinvolvedinseedgerminationandseedlingrecoveryaftersalt stress.TheTFisknowntoregulatebothABA-dependentandABA-independentactivationofOsHKT pathways(OsHKTgenefamilyisassociatedwithsaltstresstoleranceinrice)(Chenetal.,2018a).

ManyTFsregulatereproductivedevelopmentinangiosperms.FloweringislinkedwithreproductioninangiospermsandregulatedbyseveralTFsbelongingtodifferentfamiliessuchasMYB, MADS,WRKYetc.(Kumaretal.,2016;ThomsonandWellmer,2019;Zhuetal.,2020).In Chrysanthemummorifolium,floweringisregulatedbyR2R3MYBandCmMYB2TFs(Zhuetal., 2020).In A.thaliana,theinvolvementofR2R3MYB-likeTFMYB30asapositiveregulatorof floweringisreported(Liuetal.,2014).IntrinsiccrosstalkbetweenMYB30TFwiththe FLOWERINGLOCUST(FT)acceleratesfloweringbothinlongandshortdays.Likewise, TaMYB72identifiedinwheatwasfoundtoberesponsibleforshorteningoffloweringtimein rice(Zhangetal.,2016a).Onthecontrary,overexpressionofMYB44andPtrMYB192,othermembersofthesameMYBfamily,delaysfloweringinsomeplants(Jungetal.,2008;Liuetal.,2013). MembersoftheMYBfamilyalsofunctioninassociationwithotherTFs;forinstance,in Medicago sativa,SPL13downregulatestheexpressionofMsMYB112,whichcontrolsflowering(Gaoetal., 2018a).Further,MYBhasalsobeenstudiedforitsroleindevelopingflowercolor. Zhangetal. (2021) havereported PsMYB58 asapositiveanthocyaninregulatorintreepeony(Paeoniasuffruticosa Andr.)flowers.ManyinvestigationshavealsoreportedthecontributionofMADSTFsinflower development;forexample,ZmMADS69(Liangetal.,2019),LoSVP(Tangetal.,2020),CiMADS43 (Yeetal.,2021),etc.MADSdomainTFs(SUPPRESSOROFOVEREXPRESSIONOFCONSTANS1 (SOC1)/AGAMOUS-LIKE20)playsapivotalroleinpromotingfloweringin Arabidopsis (Borneretal., 2000;Leeetal.,2000).AMADSdomaingene(AGL20, AGAMOUSLIKE20)exhibitedactivationin shootapicalmeristemduringitstransitiontofloweringandwasregulatedbythegibberellinpathway. Further,itsconstitutiveexpressionin Arabidopsis offersphotoperiod-independentflowering(Borner etal.,2000).Similarly,thePeMADS5reportedfrombamboo(Phyllostachysedulis)hasbeenfoundto beresponsibleforthetransitionfromvegetativetoreproductivegrowth(Zhangetal.,2018a).Inaddition,APETALA1(AP1)andLEAFY(LFY)areothersignificantTFsthatpromotefloralmeristem developmentin Arabidopsis (Mandeletal.,1992;Weigeletal.,1992). Fruitdevelopmentisacomplexprocessandinvolvesfruit-setting,further celldivisionandexpansionfollowedbyfruitripening.Fruitripeningisavitalphenomenonaddressedmainlyforitsessentialityinthehumandietandforothercommercialaspects(Seymouretal.,2013).Fruitripeninginvolves changesintexture,color,flavor,andfragranceofthefruit.VariousTFsregulatetheseaspectsoffruit ripening,and COLORED1,C1,(a Zeamays MYB)wasthefirstTFidentifiedforitsroleinspecifying thepurplecolorofcornkernels(Paz-Aresetal.,1987).Inanearlystudy,astrongcorrelationof MdMYB10 expressionandanthocyaninaccumulationsuggesteditsroleinanthocyaninbiosynthesisin applefruits(Espleyetal.,2007).Recently,otherMYBfamilyproteinshavealsobeenidentifiedfor theirinvolvementinethylene-dependentfruitripeningintomato(Caoetal.,2020).DNA-bindingwith onefingerorDofproteinsalsocompriseawell-knownTFfamilyassociatedwithfruitripening (Khaksaretal.,2019).OthervitalTFsthatregulatefruitripeninganddevelopmentincludeFvTCP9;a TEOSINTEBRANCHED1/CYCLOIDEA/PROLIFERATING4CELLFACTORS(TCP)familymemberthatgovernsthefruitripeningprocessinstrawberries(Xieetal.,2020).ThesignificanceofNAC1 (SlNAC1)intomatofruitripeningisalsoreportedby Maetal.(2014),whichinhibitedfruitripening byregulatingethylenesynthesis andcarotenoidaccumulation.

5 1.2 Transcriptionfactorsandplantlife

Inplants,greenleavesaretheactivesitesofphotosynthesisandthusprimarilyresponsibleforplant productivity.Thedevelopmentofleavesdependsonplantspecies,developmentalstages,andenvironmentalconditions.However,leafdevelopmentisregulatedbyphytohormones,transcriptionalregulators,andtissuemechanicalproperties(BarandOri,2014).SomeoftheessentialTFsresponsiblefor leafdevelopmentareGRF,TCP,andZIP(SarvepalliandNath,2011;Bou-Torrentetal.,2012; Omidbakhshfardetal.,2015).GRFs,orGROWTH-REGULATINGFACTORS,positivelyaffectthe lateralorgangrowthandregulateleafdevelopment(Kimetal.,2003;Omidbakhshfardetal.,2015). DifferentmembersofvariousTFfamiliesareinvolvedinleafdevelopmentevents.Forexample,the WUSCHEL-RELATEDHOMEOBOX(WOX)andYABBYTFsregulateadaxial-abaxialpolarityin leaves(Rathouretal.,2020,2022;Sarojametal.,2010;Vandenbusscheetal.,2009),whereas CINCINNATA-LIKETEOSINTEBRANCHED1/CYCLOIDEA/PROLIFERATINGCELLFACTORS (CIN-TCP)familyTFsplayanessentialroleinregulatingleafpatterninganddevelopment(Koyama etal.,2007;SarvepalliandNath,2011;Alvarezetal.,2016).Similarly,theCUP-SHAPED COTYLEDONTFsfacilitateorganboundaryformationanditsorganizationandplayanimportantrole inleafdevelopment(Hassonetal.,2011).

Rootsfacilitatetheuptakeofwaterandnutrients fromthesoilandprovideanchoragetotheplants inthesoil.TheTFsthatmajorlyparticipateinrootgrowthanddevelopmentbelongtotheNAC,MYB, bHLHandMADS-boxfamilies.NAC1playsavitalroleinregulatinglateralrootformationin Arabidopsis (Xieetal.,2000).ANR1andMADS-boxTFsregulatethenitrate-induceddevelopmentof lateralroots(ZhangandForde,1998).TFsthatparticipateinroothairformationincludebHLHfamily TFsGLABRA3(GL3)/ENHANCEROFGLABRA3(EGL3)(Bernhardtetal.,2003);HBfamilymemberGLABRA2(GL2)(Masuccietal.,1996);MYBfamilyTFsCAPRICE(CPC)(Wadaetal.,1997); ENHANCEROFTRYANDCPC(etc1)(Kiriketal.,2004);TRIPTYCHON(TRY)(Schellmann etal.,2002);andWEREWOLF(WER)(LeeandSchiefelbein,1999).

1.3 Transcriptionfactorsandstressresponses

ManyTFsalsoofferstresstolerancetoplants(Table1.2).Theyusuallybindtothepromotersof stress-responsivegenesandregulatetheirexpressionlevelsinresponsetovariousabioticandbiotic stressconditionsinplants. Ngetal.(2018) reportedsixoutof58TFfamiliesinvolvedinplant responsetobioticandabioticstress.ThesemajorlyincludeAP2/ERF(APETALA2/ethyleneresponsivefactor);bHLH(basichelix-loop-helix);MYB(myeloblastosisrelated);NAC(noapical meristem,NAM; Arabidopsis transcriptionactivationfactor,ATAF1/2;cup-shapedcotyledon, CUC2);WRKY;andbZIP(basicleucinezipper).TheTFfamiliesthatmajorlycontrolthestress responsesinplantsincludeNAC,MYB,WRKY,heatshockfactors(HSFs),andAPETALA2/ Ethyleneresponsiveelementbindingfactor(AP2/ERF).NACfamilymembersareinvolvedin droughtandhighsaltstressresponseinriceand Arabidopsis (Shenetal.,2017;Yaoetal.,2018). Wangetal.(2018a) havereportedthatTaNAC30negativelyregulatesthewheatresistancetostripe rust(Pucciniastriiformis f.sp. tritici (Pst).Itssilencingviavirus-inducedgenesilencinginhibited virulent Pst isolatesCYR31colonizationandstimulatedH2O2 accumulation.Inrice,theinduction of SNAC3 wasobservedbydrought,heat,salt,andABAtreatment(Fangetal.,2015).Further,its overexpressionconferstolerancetoheat,drought,andoxidationstressandmodulationofROS 6Chapter1

Planttranscriptionfactors:anoverviewoftheirroleinplantlife