Molecular Characterization and Expression Analysis

ORIGINALPAPERMolecularCharacterizationandExpressionAnalysisofNACFamilyTranscriptionFactorsinTomatoXiaohongKou&ShuangWang&MengshiWu&RunziGuo&ZhaohuiXue&NanMeng&XiaominTao&MimiChen&YifeiZhangPublishedonline:13October2013#SpringerScience+BusinessMediaNewYork2013AbstractTheNACfamilyisconsideredoneofthelargestplant-specifictranscriptionfactorsfamilies,andfunctionsindiverseandvitalphysiologicalprocessesduringdevelopment.Inthepresentstudy,weperformedacompletebioinformaticsanalysisoftheNACfamilytranscriptionfactorsintomato,andannotatedthenon-redundantSlNAC1-74proteinsinto12sub-groups.SixNACgenesfromtomato,whichweredesignatedSNAC4–SNAC9,werestudiedinstensively.Theexpressionanal-ysisindicatedthateachSNACgeneexhibitedaspecificexpres-sionpatterninthetissuesexamined.SNAC4andSNAC6weremosthighlyexpressedinthestemsandleaves,whereastheexpressionlevelsofSNAC5,SNAC8andSNAC9werehigherinyoungleavesandoldleaves,respectively.Inaddition,theexpressionpatternsofSNACgeneswerecharacterizedduringthedevelopmentoftomatofruits.Allofthegeneswerefurtherinvestigatedtodeterminetheirresponsivenesstohormones,andacoordinatedexpressionwasobserved.TheexpressionoftheSNACgenetranscriptswasinducedbyABA,SAandshort-timeethylenetreatment,whereastheirtranscriptionwasinhibitedbyGA,6-BAandIAA.Ourpresentstudyprovidesausefulrefer-enceforfutureinvestigationsofNACgenesintomatoandotherfleshyfruits.KeywordsNAC.Transcriptionfactor.Tomato.Development.HormonesIntroductionTranscriptionfactors(TFs)areproteinsthatinteractwithDNApromotersandareinvolvedingeneexpressionandregulation.VariousplantTFs,whichcontainvariousfunction-aldomains,suchasMYB,DREBandNAC,havebeenwellstudied.TheNACgenefamilynameisanacronymderivedfromthefirstthreeidentifiedgenescontainingthisdomain:NAMfromPetuniaand,ATAF1/2andCUC2fromArabidopsis(Soueretal.1996;Aidaetal.1997).TheNACfamilymembersarecharacterizedwithahighlyconservedNACdomainregionattheN-terminalasafunctionaldomain,whichcanbefurtherdividedintofivesubdomains(A-E).TheC-terminalregionishighlyvariableinsequencecompositionandlengthand,playsavitalroleasatranscriptionalactivatororrepressor(Xieetal.2000;Ookaetal.2003;Tranetal.2004;Kimetal.2007a).Theplant-specificNACfamilyreferstoproteinscontain-ingtheNACdomain,andisoneofthelargesttranscriptionfactorfamiliesinplants.AcontinuouslyincreasingnumberofNACgeneshavebeenidentifiedandstudiedindifferentplants.Thereare105and140NACorNAC-likegenesinArabidopsisandrice,respectively,andthesecanbefurtherclassifiedinto18subfamilies(Ookaetal.2003;Fangetal.2008).Thespecificsubfamiliesarecomposedofmulti-functionalproteinsinvolvedinvariousplantbiologicalpro-cessesrelatedtogrowthanddevelopment,includingcelldivision(Kimetal.2006),seedandembryodevelopment(Duvaletal.2002;Sperotto2009),theformationoflateralrootsandcotyledons(Aidaetal.1997;Weiretal.2004;HeXiaohongKouandShuangWangmadeequalcontributionstothiswork.ElectronicsupplementarymaterialTheonlineversionofthisarticle(doi:10.1007/s11105-013-0655-3)containssupplementarymaterial,whichisavailabletoauthorizedusers.X.Kou:S.Wang(*):M.Wu:R.Guo:Z.Xue(*):N.Meng:X.Tao:M.Chen:Y.ZhangSchoolofChemicalEngineeringandTechnology,TianjinUniversity,Tianjin300072,People’sRepublicofChinae-mail:[e-mail]-mail:[e-mail](2014)32:501–516DOI10.1007/s11105-013-0655-3etal.2005),themaintenanceofshootapicalmeristems(Soueretal.1996;Aidaetal.1997;Kimetal.2007b;Maoetal.2007),organgrowthandsenescence(SablowskiandMeyerowitz1998;GuoandGan2006;Liuetal.2009;Kouetal.2012a,b),thesynthesisofsecondarywalls(Zhongetal.2007b;Koetal.2007)andplantnutritionregulation(Uauyetal.2006;Ogoetal.2008).TranscriptomestudieshaveshownthatmanyNACtran-scriptionfactorsareinvolvedintheresponsetoabioticstressandhormonaltreatments.Furthermore,someoftheNACtranscriptionfactorshavebeenreportedtobepotentialgenesfortheengineeringofstressresistanceduringtheplantlife-cycle.Interestingly,phylogeneticanalysisshowsthatmostofthestress-responsiveNACsbelongtotheATAFandAtNAC3subfamilies.TheSNAC1andSNAC2genesinricearein-ducedbycold,salinity,drought,andABA(abscisicacid)treatment,andthetransgenicplantsthatoverexpressthesegenesdemonstrateincreasedtoleranceagainstcold,salt,anddrought(Huetal.2006;Huetal.2008).SNAC2andOsNAC10canimprovetheexpressionofsomerelatedgenesunderstressconditions(Jeongetal.2010).TheANAC19,55and72genesinArabidopsisareinduciblebydrought,saltandABA,andhavebeenconfirmedtobepositiveregulatorsintheABAsignalingpathwayandstresstolerance(Tranetal.2004;Fujitaetal.2004).NACgenesarealsoinvolvedinthedefenseagainstbioticstressandareup-regulatedundercon-ditionsofpathogeninfectionandattack.IthasbeenshownthatOsNAC19inriceiselevatedbyMagnaporthegriseainfection(Linetal.2007).Tomatoisoneofthemostpopularfleshyfruitsintheworldandexhibitsawealthofnutrition.Theabundantgeneticre-sourcesavailablemaketomatoanessentialmodelsystemforthestudyofthedevelopment,ripeningandsenescenceoffleshyfruits(AlexanderandGrierson2002;Giovannoni2004;KleeandGiovannoni2011).Mostavailableresearchfocusesmainlyonmodelspecies,suchasArabidopsisandr