Transcription factor families in Arabidopsis major progress

TranscriptionfactorfamiliesinArabidopsis:majorprogressandoutstandingissuesforfutureresearch

Commentary

Li-JiaQuandYu-XianZhu

Transcriptionfactors(TFs)areagroupofproteinsthatcontrolcellularprocessesbyregulatingtheexpressionofdownstreamtargetgenes.RecentprogresshasbeenmadeinthecloningandcharacterizationofArabidopsisTFsonthegenomescale,especiallyonthecloningofopenreadingframes(ORFs),sequenceanalysisandtheexpressionpro lingofdifferentTFfamilies.HugedifferenceinnumbersofsubfamilymemberswerefoundforArabidopsisMYB,C2H2(Zn),C3H-type1(Zn),C3H-type2(Zn)TFsbyindependentresearchgroups,mainlybecauseofdifferencesinbioinformaticsearchstringency.However,theArabidopsisandricegenomescontainverydifferentnumbersofTFsintheWRKY,NAC,bZIP,MADS,ALFIN-like,GRASandC2C2(Zn)-doffamilies,indicatingapossiblepergenceofbiologicalfunctionsfromdicotstomonocots.TFshavealsobeenfoundtoplaykeyrolesinthebiosynthesisandsignalingofplanthormones,incellgrowthanddifferentiation,andinphotomorphogenesis.

Addresses

TheNationalLaboratoryofProteinEngineeringandPlantGeneticEngineering,CollegeofLifeSciences,PekingUniversity,Beijing100871,China

frontierandidentifyseveralpotentialareasoffutureresearch.

Majorprogressinrecentyears

ORFcloningandsequenceanalysisofArabidopsisTFs

CurrentOpinioninPlantBiology2006,9:544–549Availableonline31stJuly2006

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#2006ElsevierLtd.Allrightsreserved.DOI10.1016/j.pbi.2006.07.005

UsingInterProandGenBankaccessionsasfamilyiden-ti er,itwasinitiallyestimatedthattheArabidopsisgen-omecontains1533TFgenes[1].SubsequentestimatesofArabidopsisTFgenenumbersbytwoindependentgroupsvariesfrom1510to1581,mainlybecauseofdifferencesinbioinformaticsearchstringencyandde nitionsofunclas-si edTFs([2 ,3 ,4 ];Table1).Aconcertedlarge-scalecloningeffortcloned1282ORFsencodingArabidopsisTFs[2 ],andtheexpressionpro lesofover1400TFswereanalyzedusingreal-timequantitativereversetran-scriptase(qRT)-PCRtechnology[5 ].TheseORFclonesandexpressionpro leshaveenrichedourunderstandingofthecomplexityofArabidopsisTFsandtheirevolution.Thericegenomehasbeenestimatedtocontain1611TFgenes[3 ]andalargenumberoffull-lengthTFcDNAsfromricewereobtainedastheresultofagenome-widecloningproject[6].

Expressionpro lingofinpidualTFfamilies

Introduction

Byde nition,transcriptionfactors(TFs)implementtheirfunctionsbybindingdirectlytothepromotersoftargetgenesinasequence-speci cmannertoeitheractivateorrepressthetranscriptionofdownstreamtargetgenes.WiththecompletionoftheArabidopsisandricegenomesequences,itbecamepossiblenotonlytostudythefunctionofTFsonagenome-widescalebutalsotocomparethestructuralandfunctionalsimilaritiesanddifferencesbetweentheTFsofmonocotsanddicotsplants.Thenecessityforgenomicsapproachesbecomesclearasonlyabout10%oftheTFshavebeenmolecularlyorgeneticallycharacterized.Muchimportantandexcitingprogresshasbeenmadeduringthepastafewyears,includingthegenome-widecloningandcharacterizationofArabidopsisTFs,real-timeexpressionpro ling,andbioinformaticanalysisofTFsinbothArabidopsisandrice.Webrie ysummarizetherecentprogressesonthis

CurrentOpinioninPlantBiology2006,9:544–549

TheArabidopsisgenomecontainsseverallargeTFfamiliesthatincludemorethan100members,suchasMYB,MADS,basichelix-loop-helix(bHLH)andAPE-TALA2(AP2)/ETHYLENERESPONSEELEMENTBINDINGPROTEIN(EREBP)[7–10].SeveraloftheselargeTFfamilieshavebeenchosenforexpressionpro l-inganalysisinrecentyears.

MYBsuperfamily

TheMYBsuperfamilyisthelargestTFfamilyknowninplants,consistingofapproximatelyone-eighthoftheTFsinArabidopsis.Itispidedintothreefamilies,theR2R3,R1R2R3andMYB-relatedfamilies,onthebasisofthenumberandpositionoftheMYBrepeats.DifferentstudieshavepredictedthetotalnumberMYBTFstobe189[3 ],190[1]and258[2 ].Recently,163ofthemorereliableArabidopsisMYBswereclonedandstudiedsystematically[11 ].ComparedwithmammalianMYBgenes,theseplantMYBgenesaremorecomplexandperse,andonlyafewofthemexhibitedconstitutiveandubiquitousexpressioninArabidopsis[2 ,12].MYBTFsweretypicallyinvolvedinamultitudeofphysiologicalprocesses,andaccordingly,theywereinducedbyoneormoredevelop-mentalsignalsorbyenvironmentalstimuli[11 ].

http://doc.guandang.net

TranscriptionfactorfamiliesinArabidopsisQuandZhu545

bHLHfamily

Atotalof162AtBHLHgeneshavebeenidenti ed,makingitthesecondlargestTFfamilyintheArabidopsisgenome[10].MembersofthisTFfamilyareknowntobeinvolvedincontrollingcellproliferationandinthedevelopmentofspeci ccelllineages[13].Theirmechanismforregulatingtranscriptionofteninvolvestheformationofhomo-orhetero-dimericcon gurationsthatcanbindspeci callytotheG-boxDNAsequencemotifCACGTG[14].

AP2/EREBPfamily

successfullyampli edandclonedfromvarioustypesofArabidopsistissuesororgansorafterdifferenttreatments;hence,theAP2/EREBPfamilyisthemostcompletelyclonedArabidopsisTFfamilytodate[15 ].AlthoughmanyAP2/EREBPmembersareexpressedinatissue-speci cmannerand/orexpresseddifferentiallyinresponsetodifferentphytohormones[15 ],itisbelievedthatthisgenefamilyaremainlyinvolvedinresponsestodifferentstresses:drought,freezingandpathogeninva-sion[16].

MADSfamily

TheArabidopsisgenomecontains147membersoftheAP2/EREBPfamily,whicharepidedintothreesub-groups[15 ].Atotalof145AP2/EREBPTFshavebeen

http://doc.guandang.net

TheArabidopsisMADSfamilyiscomposedofabout100members.MostArabidopsisMADSTFsareinvolved

CurrentOpinioninPlantBiology2006,9:544–549

546Commentary

intheregulationof ower-relatedphysiologicalanddevelopmentalprocesses[17].Membersofthissuper-familywerepredominantlydetectedin owersandfruits[12].

WRKYfamily

indicator[23].Also,quiteafewTFs,suchasARFs,PIF1andPIF3,arenowknowntoberegulatedmainlybyaproteosome-mediatedproteindegradationandturnoverpathway[24 ,25,26 ].

EvolutionofTFs

TherearetwocontradictoryhypothesesregardingtheevolutionoftheMYBsuperfamily.The rsthypothesisstatesthatR2R3TFsarerelativelynewandp …… 此处隐藏：23622字，全部文档内容请下载后查看。喜欢就下载吧 ……