Genomic Survey and Gene Expression Analysis of

GenomeAnalysisGenomicSurveyandGeneExpressionAnalysisoftheBasicLeucineZipperTranscriptionFactorFamilyinRice1[W][OA]AashimaNijhawan,MukeshJain,AkhileshK.Tyagi,andJitendraP.Khurana*InterdisciplinaryCentreforPlantGenomicsandDepartmentofPlantMolecularBiology,UniversityofDelhiSouthCampus,NewDelhi110021,IndiaThebasicleucine(Leu)zipper(bZIP)proteinscomposeafamilyoftranscriptionalregulatorspresentexclusivelyineukaryotes.ThebZIPproteinscharacteristicallyharborabZIPdomaincomposedoftwostructuralfeatures:aDNA-bindingbasicregionandtheLeuzipperdimerizationregion.Theyhavebeenshowntoregulatediverseplant-specificphenomena,includingseedmaturationandgermination,floralinductionanddevelopment,andphotomorphogenesis,andarealsoinvolvedinstressandhormonesignaling.Wehaveidentified89bZIPtranscriptionfactor-encodinggenesintherice(Oryzasativa)genome.TheirchromosomaldistributionandsequenceanalysessuggestthatthebZIPtranscriptionfactorfamilyhasevolvedviageneduplication.ThephylogeneticrelationshipamongricebZIPdomainsaswellaswithbZIPdomainsfromotherplantbZIPfactorssuggeststhathomologousbZIPdomainsexistinplants.Similarintron/exonstructuralpatternswereobservedinthebasicandhingeregionsoftheirbZIPdomains.DetailedsequenceanalysishasbeendonetoidentifyadditionalconservedmotifsoutsidethebZIPdomainandtopredicttheirDNA-bindingsitespecificityaswellasdimerizationproperties,whichhashelpedclassifythemintodifferentgroupsandsubfamilies,respectively.ExpressionofbZIPtranscriptionfactor-encodinggeneshasbeenanalyzedbyfull-lengthcDNAandexpressedsequencetag-basedexpressionprofiling.Thisexpressionprofilingwascomplementedbymicroarrayanalysis.TheresultsindicatespecificorcoexpressionpatternsofricebZIPtranscriptionfactorsstartingfromfloraltransitiontovariousstagesofpanicleandseeddevelopment.bZIPtranscriptionfactor-encodinggenesinricealsodisplayeddifferentialexpressionpatternsinriceseedlingsinresponsetoabioticstressandlightirradiation.AnefforthasbeenmadetolinkthestructureandexpressionpatternofbZIPtranscriptionfactor-encodinggenesinricetotheirfunction,basedontheinformationobtainedfromouranalysesandearlierknownresults.ThisinformationwillbeimportantforfunctionalcharacterizationofbZIPtranscriptionfactorsinrice.Severalfamiliesoftranscriptionfactorshavebeenidentifiedbothinanimalsaswellasplants.ThebasicLeuzipper(bZIP)transcriptionfactorfamilyisamongthelargestandmostdiversedimerizingtranscriptionfactorfamilies.bZIPtranscriptionfactorsowetheirnametotheirhighlyconservedbZIPdomaincom-posedofabasicregionandaLeuzipper(Hurst,1994).ThebZIPdomainis60to80aminoacidsinlength.Thebasicregionconsistsofabout16aminoacidresiduescharacterizedbythepresenceofaninvariantN-x7-R/Kmotif,whereastheLeuzipperiscomposedofheptadrepeatsofLeuorotherbulkyhydrophobicaminoacids(Ile,Val,Phe,orMet)positionedexactlynineaminoacidstowardtheCterminus.ThebasicandLeuzipperregionsarefunctionallydistinct.Thebasicregionisresponsibleforsequence-specificDNAbindingandishighlyconserved.TheLeuzipperisanamphipathicsequenceintheformofcoiled-coil,whichconfersdimerizationspecificityandislessconserved.ThisLeuzippersequencemediateshomo-and/orhetero-dimerizationinbZIPproteins.bZIPmonomersareintheformoflonga-helices,and,atthetimeofDNAbinding,theN-terminalhalfbindsinthemajorgroovetodouble-strandedDNA,whereastheC-terminalhalfmediatesdimerizationtoformasuperimposedcoiled-coilstructurecalledtheLeuzipper(Landschulzetal.,1988;Ellenbergeretal.,1992).bZIPtranscriptionfactor-encodinggeneshavebeenidentifiedexclusivelyineukaryotes.Theirnumberis17inSaccharomycescerevi-siae,31inCaenorhabditiselegans,27inDrosophila,56inhumans,and67inArabidopsis(Arabidopsisthaliana)genomes(Riechmannetal.,2000;Fassleretal.,2002;Vinsonetal.,2002;Deppmannetal.,2004).Inplants,likeothertranscriptionfactorgenes,mem-bersofthebZIPtranscriptionfactorfamilyarealsoeitherexpressedconstitutivelyorinanorgan-specific(Schindleretal.,1992a;Rodriguez-UribeandO’Connell,2006),stimulus-responsive(deVettenandFerl,1995),development-dependent(Chernetal.,1996),andcell-cycle-specific(Minamietal.,1993)manner.Sofar,over1ThisworkwassupportedbytheDepartmentofBiotechnology,GovernmentofIndia,theUniversityGrantsCommission,andtheCouncilofScientificandIndustrialResearch,NewDelhi(researchfellowshiptoA.N.).*Correspondingauthor;[e-mail]istributionofmaterialsintegraltothefindingspresentedinthisarticleinaccordancewiththepolicydescribedintheInstructionsforAuthors()is:JitendraP.Khurana([e-mail]).[W]TheonlineversionofthisarticlecontainsWeb-onlydata.[OA]OpenAccessarticlecanbeviewedonlinewithoutasub-scription.–350,2007AmericanSocietyofPlantBiologists333120bZIPtranscriptionfactorshavebeenidentifiedindifferentplants(SupplementalTableS1).Inmanyplants,bZIPtranscriptionfactorshavebeenreportedtofunctionintheregulationofseedmaturationandgermination(Izawaetal.,1994;Chernetal.,1996).Availablefunctionalinformationsuggeststheirrolenotonlyinthe