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RhythmsofLife ThePlantCircadianClock Somers D E 1999 Thephysiologyandmolecularbasesoftheplantcircadianclock PlantPhysiol 121 9 20 Livingonarotatingplanetisbiologicallystressful Overa24hourperiodthereislargevariationinenvironmentalconditionsincludingtemperature lightintensity humidityandpredatorbehavior SeeKudoh H 2016 Molecularphenologyinplants innaturasystemsbiologyforthecomprehensiveunderstandingofseasonalresponsesundernaturalenvironments NewPhytol 210 399 412 Image NASA Extremeday nighttemperaturedifference 57oC 48oCto9oC Montana 1972 Typicalday nightfluctuation 10oCeachday centralJapan Circadianclocksarebiologicaloscillatorswitha 24hourperiod Higherlevelsofwheelrunningactivityatnight Incontinuousdarknesstheserhythmspersistbutwitha 23hourperiod FigurefromLi J D Burton K J Zhang C Hu S B andZhou Q Y 2009 VasopressinreceptorV1aregulatescircadianrhythmsoflocomotoractivityandexpressionofclock controlledgenesinthesuprachiasmaticnuclei Am J Physiol 296 R824 R830 usedwithpermission Imagesource Mylius Inactive Active Circadianclockscontrolmanyaspectsofhumanphysiology Imagesource Addicted04 Plantcircadianbiologyhasalonghistory Illustrationof sleep movementsinMedicago fromCharlesDarwin 1880 ThePowerofMovementinPlants Imagesources H Zell CharlesDarwin PowerofMovementinPlants DeMarian 1729 Observationbotanique ofMimosapudica sensitivetotheSunanddaylight theleaves theirpedunclesfoldthemselvesaway contractaroundsunset inthesamewaytheydowhenthePlantistouchedorshaken Architectureofthecircadianclock Principlesofoperationofplantcircadianclocks Interconnectedpartsofthecircadiansystem Circadianoscillator Entrainmentpathways Outputpathways Gene Rhythmsin transcription physiology biochemistry EnvironmentalInputs Circadiangatingofentrainmentandoutputs Thecircadianoscillator Mostcircadianclocksaretranscription translationfeedbackloops GeneA GeneB ProteinA TheproteinencodedbyGeneAactivatesGeneB Thecircadianoscillator 0 12 24 36 48 GeneA GeneB ProteinA Genetranscriptabundance Thefeedbackloopresultsinrhythmsoftranscriptabundanceofthetwogenes Time hours GeneA GeneB AnearlymodelforthefunctioningofthecircadianclockinArabidopsis FromAlabad D Oyama T Yanovsky M J Harmon F G M s P andKay S A 2001 ReciprocalregulationbetweenTOC1andLHY CCA1withintheArabidopsiscircadianclock Science 293 880 883 ReprintedwithpermissionfromAAAS ThisisoneofthefirststructuresproposedfortheplantcircadianclockItisanoscillatorwithactivationandsuppressionfeedback comparewithpreviousslide ThemaingenesinvolvedareTOC1 LHYandCCA1Themodelisoutofdate TOC1actuallysuppressesCCA1 butprovidesanexampleofoscillatorstructure GeneA ProteinA GeneB ProteinB Activation outofdate Suppression ReciprocalrepressionbetweenCCA1andTOC1atthecoreofthecircadianclock FromAlabad D Oyama T Yanovsky M J Harmon F G M s P andKay S A 2001 ReciprocalregulationbetweenTOC1andLHY CCA1withintheArabidopsiscircadianclock Science 293 880 883 ReprintedwithpermissionfromAAAS Gendron J M Pruneda Paz J L Doherty C J Gross A M Kang S E andKay S A 2012 Arabidopsiscircadianclockprotein TOC1 isaDNA bindingtranscriptionfactor Proc Natl Acad Sci USA109 3167 3172 OverexpressionofCCA1suppressescircadianoscillationsofTOC1CCA1andLHYbindtothepromoterofTOC1 OverexpressionofTOC1suppressescircadianoscillationsofCCA1TheCCTdomainofTOC1isrequiredforittobindtheCCA1promoter Thecurrentmodelofthecircadianoscillatorisacomplexnetwork EveningComplex ReprintedfromHsu P Y andHarmer S L 2014 Wheelswithinwheels theplantcircadiansystem TrendsPlantSci 19 240 249withpermissionfromElsevier MorningLoop NoteTOC1isasuppressorofCCA1 LHY comparewithpreviousmodel Differentclockcomponentsareexpressedatdifferenttimesofday Networkmodelsindicateconnectionsbetweencomponents butlacktemporalinformationaboutclockfunctionThisexampleshowshowthreeclockgenesareactivatedatdifferenttimesofday night ReprintedfromHsu P Y andHarmer S L 2014 Wheelswithinwheels theplantcircadiansystem TrendsPlantSci 19 240 249withpermissionfromElsevier DatafromDIURNALdatabase http diurnal mocklerlab org Thecircadianclockalsoincludespost transcriptionalprocesses Chromatinremodeling e g promoterofTOC1hasaclock controlledpatternofhistone3 H3 acetylationthataffectsTOC1expressionControlofproteinstabilitybyproteasome e g ZTLisinvolvedindark dependentdegradationoftheTOC1protein Phosphorylation e g CaseinKinase2 CK2 phosphorylatesCCA1andLHYCytosolicsignalingmolecules e g circadianrhythmsofcADPRandCa2 inthecytosolregulatethedynamicsoftheoscillator SeeM s P 2008 CircadianclockfunctioninArabidopsisthaliana timebeyondtranscription TrendsCellBiol 18 273 281forreview Thecircadianoscillatoristemperature compensated Temperature oC Col 0wildtypemaintainsa 24periodacrossarangeoftemperatures i e istemperaturecompensated PRR7 PRR9knockdownchangesperiodinresponsetotemperaturechange Salom P A Weigel D andMcClung C R 2010 TheroleoftheArabidopsisMorningloopcomponentsCCA1 LHY PRR7 andPRR9intemperaturecompensation PlantCell 22 3650 3661 Nagel D H Pruneda Paz J L andKay S A 2014 FBH1affectswarmtemperatureresponsesintheArabidopsiscircadianclock Proc Natl Acad Sci USA111 14595 14600 PRR7 PRR9andFBH1haverolesintemperaturecompensation Whyisentrainmentrequired Thetimeofdawnandduskisdifferenteverysingleday Timeofsunrise Timeofsunset Dayofyear Timeofday 24hclock Location Bristol UK51 4500 N 2 5833 W Whyisentrainmentrequired Theperiodofthecircadianoscillatorisapproximately24handthereisnaturalvariationbetweenplants Circadianperiod h Measurements ReprintedfromSwarup K Alonso Blanco C Lynn J R Michaels S D Amasino R M Koornneef M andMillar A J 1999 NaturalallelicvariationidentifiesnewgenesintheArabidopsiscircadiansystem PlantJ 20 67 77 MeasurementsofcircadianperiodinthreewildtypestrainsofArabidopsisthalianaThereisvariationwithinandbetweenstrains butallhaveaperiodofapproximately24hours Severalenvironmentalsignalsentrainthecircadianoscillator Circadianoscillator Redlight phytochromephotoreceptors Bluelight cryptochromephotoreceptors Sugarsproducedbyphotosynthesis Temperaturefluctuations Phytochromesandcryptochromesprovidelightinputtothecircadianclock cry1mutant cry2mutant Fluencerateofbluelight molm 2s 1 Wildtype Wildtype FromSomers D E Devlin P F andKay S A 1998 PhytochromesandcryptochromesintheentrainmentoftheArabidopsiscircadianclock Science 282 1488 1490ReprintedwithpermissionfromAAAS Fluencerateofredlight molm 2s 1 Wildtype phyBmutant Wildtype Circadianclocksregulateplantcellsbycontrollinggeneexpression Somecircadianclockproteinsaretranscriptionfactorsthatregulatesetsofgeneswithacircadianrhythm Example adaytimetranscriptionfactor Day Night Specificgenepromotersequencesmayunderliespecificcircadianphasesoftranscription TheseciselementsoccurwithhighfrequencyinpromotersoftranscriptsetswithcertaincircadianphasesIndicatesthatthecircadianclockregulatesdifferentsubsetsofgeneswithdifferentcircadianphasesthroughparticularclock controlledpromotermotifs Covington M F Maloof J N Straume M Kay S A andHarmer S L 2008 Globaltranscriptomeanalysisrevealscircadianregulationofkeypathwaysinplantgrowthanddevelopment GenomeBiology 9 1 18 Theimportanceofcircadianrhythmsinplantbiology Plantswithafunctioningcircadianclockthatmatchestheenvironmentgrowlarger FromDodd A N Salathia N Hall A K vei E T th R Nagy F Hibberd J M Millar A J andWebb A A R 2005 Plantcircadianclocksincreasephotosynthesis growth survival andcompetitiveadvantage Science 309 630 633 ReprintedwithpermissionfromAAAS Thecircadianclockcontrolsmultipleaspectsofplantbiology MolecularBiology 30 oftheArabidopsisthalianatranscriptomeoscillateswitha24period FromHarmer S L Hogenesch J B Straume M Chang H S Han B Zhu T Wang X Kreps J A andKay S A 2000 OrchestratedtranscriptionofkeypathwaysinArabidopsisbythecircadianclock Science 290 2110 2113andfromDodd A N Salathia N Hall A K vei E T th R Nagy F Hibberd J M Millar A J andWebb A A R 2005 Plantcircadianclocksincreasephotosynthesis growth survival andcompetitiveadvantage Science 309 630 633 ReprintedwithpermissionfromAAAS Thecircadianclockcontrolsmultipleaspectsofplantbiology Development Photoperiodisoneoftheenvironmentalfactorscontrollingflowering ReprintedwithpermissionfromfromDowson Day M J andMillar A J 1999 CircadiandysfunctioncausesaberranthypocotylelongationpatternsinArabidopsis PlantJ 17 63 71andAmasino R 2010 Seasonalanddevelopmentaltimingofflowering PlantJ 61 1001 1013 Thecircadianclockgivesplantsafitnessadvantage 20h 28h 20h 28h Competitionexperiments Whentheendogenousperiodmatchestheexternallight darkcycles plantsperformbetterintermsof survivalbiomass dryandfreshweight chlorophyllcontent Arabidopsisthalianamutantlineswithendogenouscircadianperiod FromDodd A N Salathia N Hall A K vei E T th R Nagy F Hibberd J M Millar A J andWebb A A R 2005 Plantcircadianclocksincreasephotosynthesis growth survival andcompetitiveadvantage Science 309 630 633 ReprintedwithpermissionfromAAAS Endogenousperiod Environment Investigatingthecircadianclockinthelaboratory Time courseanalysisisusedtostudycircadianrhythmsinplants Theplantisfirstgrownincyclesoflightanddark Theplantisthentransferredtoconditionsofconstantlight ordark andtemperature wherecircadian regulatedbiologicalprocesswill freerun Thetimethatwouldhavebeendarkisreferredtoas subjectivenight andissometimesindicatedbygreybarsoncircadiantime courses Time h Circadianrhythmshaveanumberofmeasurableproperties 60 72 84 96 Biologicalprocess Period Amplitude Phase timeofpeakrelativetosubjectivedawn Time h Period timetocompleteonefullcyclePhase thetimeatwhichaparticularpointofcycleoccurs e g thepeak Amplitude thedisplacementoftheoscillationfromthecenterpoint Subjectivedawn occursevery24hafterlightson Commonmethodsforstudyingcircadianrhythms Transcriptanalysis Individualtranscriptscanbemonitored CircadianrhythmsofthewholetranscriptomecanbestudiedwithmicroarraysorRNAsequencing or PhotosystemIandIItranscripts Lightharvestingcomplextranscripts FromHarmer S L Hogenesch J B Straume M Chang H S Han B Zhu T Wang X Kreps J A andKay S A 2000 OrchestratedtranscriptionofkeypathwaysinArabidopsisbythecircadianclock Science 290 2110 2113 ReprintedwithpermissionfromAAAS Thistranscriptomeanalysisfoundthatmanyphotosynthesisgeneshavecircadianrhythms Non invasivemeasurementtechniquesbenefitthestudyofcircadianrhythms Measurementsofabiologicalpropertyneedtobemadefrequently e g hourly overseveraldaysDestructivesamplingtoobtainRNAorproteinisinconvenient Substantialquantitiesofplantmaterialrequired longworkinghours opportunitiesforhumanerrorNon invasiveandautomatedmeasurementtechniqueshavebeendevelopedDestructivesamplingissometimesessentialtomonitorrhythmsoftranscripts proteinsormetabolites Commonmethodsforstudyingcircadianrhythms Leafmovement FromHicks K A Millar A J Carr I A Somers D E Straume M Meeks Wagner D R andKay S A 1996 ConditionalcircadiandysfunctionoftheArabidopsisearly flowering3mutant Science 274 790 792 ReprintedwithpermissionfromAAAS Imagecredits Vojt chZavadil K Hubbardunpublished Leafposition pixels 0 24 48 72 96 120 144 Automatedvideoimagingandimageanalysisallowsquantificationofleafmovements Someplantshaveapulvinusatthebaseoftheleafwhichdrivesmovementoftheleaves InArabidopsis leafmovementsarepartofrhythmicpatternsingrowth Commonmethodsforstudyingcircadianrhythms Bioluminescenceimaging Expressioninplantsofanenzymefromfirefliescalledluciferasecausesplantstoemitlightwhenprovidedwiththesubstrateluciferin LUCIFERASE Luciferin O2 ATP Light Oxyluciferin AMP LUCIFERASEtransgene Plantgenome Commonmethodsforstudyingcircadianrhythms Bioluminescenceimaging PlacingLUCIFERASEunderthecontrolofapromoterwithacircadianrhythmallowstherhythmtobemonitored Theplantemitscircadianrhythmsoflightthatcanbedetectedwithaverysensitivecamera LuciferasebioluminescenceimagedfromArabidopsisseedlings Millar A J Short S R Chua N H andKay S A 1992 Anovelcircadianphenotypebasedonfireflyluciferaseexpressionintransgenicplants PlantCell 4 1075 1087 Commonmethodsforstudyingcircadianrhythms Bioluminescenceimaging FromMillar A Carre I Strayer C Chua N andKay S 1995 CircadianclockmutantsinArabidopsisidentifiedbyluciferaseimaging Science 267 1161 1163 ReprintedwithpermissionfromAAAS LUCIFERASEisplacedunderthecontroloftherhythmicCAB2promoterAround8000seedlingsfromamutagenizedpopulationweretested toidentifycomponentsofthecircadianclockThisallowedidentificationofcircadianclockcomponents here TOC1 Mutantwithshortcircadianperiod toc1 1 Wildtypeseedlings Advancedmethodsforstudyingcircadianrhythms Rhythmsinindividualtissues 1 Useasupersensitivecamerawithcloseuplenstomonitorluciferase Bioluminescencefromindividualpixels LuciferasebioluminescencefromsingleArabidopsisleaf Wenden B Toner D L K Hodge S K Grima R andMillar A J 2012 Spontaneousspatiotemporalwavesofgeneexpressionfrombiologicalclocksintheleaf Proc Natl Acad Sci USA 109 6757 6762 Advancedmethodsforstudyingcircadianrhythms Rhythmsinindividualtissues 2 Splitluciferaseintotwofragments andgiveoneatissue specificgenepromoter Thishalfofluciferaseisonlyexpressedwhentheclockpromoterisactive Thishalfofluciferaseisonlyexpressedinthespecifictissuetype ReprintedbypermissionfromMacmillanPublishersLtd Endo M Shimizu H Nohales M A Araki T andKay S A 2014 Tissue specificclocksinArabidopsisshowasymmetriccoupling Nature 515 419 422 Advancedmethodsforstudyingcircadianrhythms Rhythmsinindividualtissues Onehalfofluciferase VascularSUC2promoter Onehalfofluciferase CircadianTOC1promoter Thiswasusedtoshowthecircadianclockinvasculartissueisdominanttothatofothercelltypesinleaves 1mm 2 Splitluciferaseintotwofragments andgiveoneatissue specificgenepromoter ReprintedbypermissionfromMacmillanPublishersLtd Endo M Shimizu H Nohales M A Araki T andKay S A 2014 Tissue specificclocksinArabidopsisshowasymmetriccoupling Nature 515 419 422 Advancedmethodsforstudyingcircadianrhythms Thevalueofmathematicalmodeling Howdoyouunravelhowthisfunctions It stotallynon intuitive LargenumberofinterconnectedclockcomponentsMultiplefeedbackloops bothpositiveandnegativeEachproteinandtranscripthasitsownuniquerateofsynthesisandbreakdown ReprintedfromHsu P Y andHarmer S L 2014 Wheelswithinwheels theplantcircadiansystem TrendsPlantSci 19 240 249withpermissionfromElsevier Advancedmethodsforstudyingcircadianrhythms Thevalueofmathematicalmodeling Buildingmathematicalsimulationsoftheclockhas ProvidednewinformationabouthowclockcomponentsinteractProvidedexplanationsforwhytheclockissocomplexProvidednewinformationabouthowtheclockisentrainedtotheenvironmentDemonstratedthepowerofmathematicalandsystemsbiologyapproachesforbiologicalresearch Thecircadianclockandplantmetabolism Thecircadianclockhasextensivecontrolofplantmetabolism Almostallmetabolicpathwaysincludeatleastoneenzymethatisundercircadiantranscriptionalcontrol Eachsquare Onecircadian regulatedtranscriptColorofsquare phaseofexpression ReprintedfromFarr E M andWeise S E 2012 Theinteractionsbetweenthecircadianclockandprimarymetabolism Curr Opin PlantBiol 15 293 300withpermissionfromElsevier Manymetabolicpathwayshavephysiologicallyappropriatephasesofmaximaltranscriptabundance DatafromDIURNALdatabase http diurnal mocklerlab org ChlorophyllbiosynthesisgenespeakjustbeforedawntoanticipatelightavailabilityStarchcatabolismgenespeakarounddusk Circadianclockmutantshavealteredmetabolitelevelsinlight darkcycles Datashownforaprr9 7 5triplemutantgrownin12hlight 12hdarkcycles IncreaseinCitricAcidCycleintermediates IncreaseinShikimatesuggestschangesinsecondarymetabolism Fukushima A Kusano M Nakamichi N Kobayashi M Hayashi N Sakakibara H Mizuno T andSaito K 2009 Impactofclock associatedArabidopsispseudo responseregulatorsinmetaboliccoordination Proc Natl Acad Sci USA106 7251 7256 Carbohydratedegradationatnightistemporallycontrolled Therateofstarchdegradationisrelatedtothelengthofthenight sothattheplantonlyexhaustsstarchreservesjustbeforetheendofthenight Graf A Schlereth A Stitt M andSmith A M 2010 CircadiancontrolofcarbohydrateavailabilityforgrowthinArabidopsisplantsatnight Proc Natl Acad Sci USA107 9458 9463 cca1 lhymutantsexhauststarchreservesatnight cca1 lhymutants Accumulate20 lessstarchthanwildtypesDegradestarch35 fasterthanwildtypesatnightExhauststarchreserves3 4hoursbeforetheendofthenightExpressstarvationgenesbeforetheendofthenight Graf A Schlereth A Stitt M andSmith A M 2010 CircadiancontrolofcarbohydrateavailabilityforgrowthinArabidopsisplantsatnight Proc Natl Acad Sci USA107 9458 9463 Thechloroplasthascircadianrhythmsofgeneexpressionthatarecontrolledbythenucleus psbD Chloroplastgene SIG5 Nucleargene chloroplast FromNoordally Z B Ishii K Atkins K A Wetherill S J Kusakina J Walton E J Kato M Azuma M Tanaka K Hanaoka M andDodd A N 2013 Circadiancontrolofchloroplasttranscriptionbyanuclear encodedtimingsignal Science 339 1316 1319 ReprintedwithpermissionfromAAAS Primarymetabolitesregulatetheactivityofthecircadianoscillator Dalchau N Baek S J Briggs H M Robertson F C Dodd A N Gardner M J Stancombe M A Haydon M J Stan G B Gon alves J M andWebb A A R 2011 ThecircadianoscillatorgeneGIGANTEAmediatesalong termresponseoftheArabidopsisthalianacircadianclocktosucrose Proc Natl Acad Sci USA108 5104 5109 Applicationofexternalsucroserestorescircadianrhythmsinwildtypeseedlingsgrowninthedark ThisisdependentonthepresenceoftheoscillatorcomponentGIGANTEA Theoscillator environmentalsignallingandmetabolismformanintegratednetwork ImagebasedonFarr E M andWeise S E 2012 Theinteractionsbetweenthecircadianclockandprimarymetabolism Curr Opin PlantBiol 15 293 300andHaydon M J Hearn T J Bell L J Hannah M A andWebb A A R 2013 Metabolicregulationofcircadianclocks Semin CellDevel Biol 24 414 421 CentralOscillatorCCA1PRR7 5 9GITOC1 Metabolism EnvironmentalSignalling ChloroplastsPhotosynthesisSugarRedoxATP NAD MitochondriaRedoxATP NAD NAD LightTemperature Thecircadianclockregulatesproductionofvolatilecompounds Petuniasusetheemissionofvolatilecompoundstoattractnocturnalpollinatorssuchashawkmoths Therearecircadianrhythmsofvolatileemissions gemitted gfreshweight hr Fenske M P HewettHazelton K D Hempton A K Shim J S Yamamoto B M Riffell J A andImaizumi T 2015 CircadianclockgeneLATEELONGATEDHYPOCOTYLdirec