Plant Physiol Chapter 14 - Gene Expression and Sig

1PLANTBIOLOGISTSMAYBEFORGIVENfortakingabidingsat-isfactioninthefactthatMendel’sclassicstudiesontheroleofher-itablefactorsindevelopmentwerecarriedoutonafloweringplant:thegardenpea.TheheritablefactorsthatMendeldiscovered,whichcontrolsuchcharactersasflowercolor,flowerposition,podshape,stemlength,seedcolor,andseedshape,cametobecalledgenes.GenesaretheDNAsequencesthatencodetheRNAmoleculesdirectlyinvolvedinmakingtheenzymesandstructuralproteinsofthecell.Genesarearrangedlinearlyonchromosomes,whichformlinkagegroups—thatis,genesthatareinheritedtogether.ThetotalamountofDNAorgeneticinformationcontainedinacell,nucleus,ororganelleistermeditsgenome.SinceMendel’spioneeringdiscoveriesinhisgarden,theprinci-plehasbecomefirmlyestablishedthatthegrowth,development,andenvironmentalresponsesofeventhesimplestmicroorganismaredeterminedbytheprogrammedexpressionofitsgenes.Amongmulticellularorganisms,turninggeneson(geneexpression)oroffaltersacell’scomplementofenzymesandstructuralproteins,allowingcellstodifferentiate.Inthechaptersthatfollow,wewilldiscussvariousaspectsofplantdevelopmentinrelationtothereg-ulationofgeneexpression.Variousinternalsignalsarerequiredforcoordinatingtheexpres-sionofgenesduringdevelopmentandforenablingtheplanttorespondtoenvironmentalsignals.Suchinternal(aswellasexternal)signalingagentstypicallybringabouttheireffectsbymeansofsequencesofbiochemicalreactions,calledsignaltransductionpath-ways,thatgreatlyamplifytheoriginalsignalandultimatelyresultintheactivationorrepressionofgenes.Muchprogresshasbeenmadeinthestudyofsignaltransductionpathwaysinplantsinrecentyears.However,beforedescribingwhatGeneExpressionandSignalTransduction14CHAPTER142isknownaboutthesepathwaysinplants,wewillprovidebackgroundinformationongeneexpressionandsignaltransductioninotherorganisms,suchasbacteria,yeasts,andanimals,makingreferencetoplantsystemswhereverappropriate.Thesemodelswillprovidetheframeworkfortherecentadvancesinthestudyofplantdevelopmentthatarediscussedinsubsequentchapters.GenomeSize,Organization,andComplexityAsmightbeexpected,thesizeofthegenomebearssomerelationtothecomplexityoftheorganism.Forexample,thegenomesizeofE.coliis4.7×106bp(basepairs),thatofthefruitflyis2×108bpperhaploidcell,andthatofahumanis3×109bpperhaploidcell.However,genomesizeineukaryotesisanunreliableindicatorofcomplex-itybecausenotalloftheDNAencodesgenes.Inprokaryotes,nearlyalloftheDNAconsistsofuniquesequencesthatencodeproteinsorfunctionalRNAmolecules.Inadditiontouniquesequences,how-ever,eukaryoticchromosomescontainlargeamountsofnoncodingDNAwhosemainfunctionsappeartobechromosomeorganizationandstructure.MuchofthisnoncodingDNAconsistsofmulticopysequences,calledrepetitiveDNA.TheremainderofthenoncodingDNAismadeupofsingle-copysequencescalledspacerDNA.Together,repetitiveandspacerDNAcanmakeupthemajorityofthetotalgenomeinsomeeukaryotes.Forexample,inhumansonlyabout5%ofthetotalDNAconsistsofgenes,theuniquesequencesthatencodeforRNAandproteinsynthesis.Thegenomesizeinplantsismorevariablethaninanyothergroupofeukaryotes.Inangiosperms,thehap-loidgenomerangesfromabout1.5×108bpforAra-bidopsisthaliana(smallerthanthatofthefruitfly)to1×1011bpforthemonocotTrillium,whichisconsiderablylargerthanthehumangenome.EvencloselyrelatedbeansofthegenusViciaexhibitgenomicDNAcontentsthatvaryovera20-foldrange.Whyareplantgenomessovariableinsize?StudiesofplantmolecularbiologyhaveshownthatmostoftheDNAinplantswithlargegenomesisrepet-itiveDNA.Arabidopsishasthesmallestgenomeofanyplantbecauseonly10%ofitsnuclearDNAisrepetitiveDNA.ThegenomesizeofriceisestimatedtobeaboutfivetimesthatofArabidopsis,yetthetotalamountofuniquesequenceDNAinthericegenomeisaboutthesameasinArabidopsis.ThusthedifferenceingenomesizebetweenArabidopsisandriceisduemainlytorepet-itiveandspacerDNA.MostPlantHaploidGenomesContain20,000to30,000GenesUntilrecently,thetotalnumberofgenesinanorgan-ism’sgenomewasdifficulttoassess.Thankstorecentadvancesinmanygenomicsequencingprojects,suchnumbersarenowbecomingavailable,althoughprecisevaluesarestilllacking.AccordingtoMiklosandRubin(1996),thenumberofgenesinbacteriavariesfrom500to8,000andoverlapswiththenumberofgenesinmanysimpleunicellulareukaryotes.Forexample,theyeastgenomeappearstocontainabout6,000genes.Morecomplexeukaryotes,suchasprotozoans,worms,andflies,allseemtohavegenenumbersintherangeof12,000to14,000.TheDrosophila(fruitfly)genomecon-tainsabout12,000genes.Thus,thecurrentviewisthatittakesroughly12,000basictypesofgenestoformaeukaryoticorganism,althoughvaluesashighas43,000genesarecommon,asaresultofmultiplecopiesofcer-taingenes,ormultigenefamilies.Thebest-studiedplantgenomeisthatofArabidop-sisthaliana.ChrisSomervilleandhiscolleaguesatStan-fordUniversityhaveestimatedthattheArabidopsisgenomecontainsroughly20,000genes(Rounsleyetal.1996).Thisestimateisbasedonmorethanoneapproach.Forexample,sincelargeregionsofthegenomehavebeensequenced,weknowthereisonegeneforevery5kb(kilobases)ofDNA.Sincetheentiregenomecontainsabout100,000kb,theremustbeabout20,000genes.However,6%ofthegenomeencodesribosomalRNA,andanother2%consistsofhighly