PLANT CHEMICAL GENOMICS : methods and protocols. PDF
Preview PLANT CHEMICAL GENOMICS : methods and protocols.
Methods in Molecular Biology 2213 Glenn R. Hicks Chunhua Zhang Editors Plant Chemical Genomics Methods and Protocols Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences, University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Plant Chemical Genomics Methods and Protocols Second Edition Edited by Glenn R. Hicks Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA Chunhua Zhang Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA Editors GlennR.Hicks ChunhuaZhang DepartmentofBotany DepartmentofBotany andPlantSciences andPlantPathology InstituteofIntegrative CenterforPlantBiology GenomeBiology PurdueUniversity UniversityofCalifornia WestLafayette,IN,USA Riverside,CA,USA ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-0716-0953-8 ISBN978-1-0716-0954-5 (eBook) https://doi.org/10.1007/978-1-0716-0954-5 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2014,2021 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface ThefirsteditionofPlantChemicalGenomics:MethodsandProtocolswaspublishedin2014. Atthattime,theuseofchemicalgenomicswasrapidlydevelopingwithcriticalsuccessstories leadingtoanenhancedunderstandingofplantstress,pathogenresponses,endomembrane trafficking,hormonesignaling,andotherareasinplantbiology.Asaresult,thefocusofthat edition was on sharing with the scientific community approaches to screen synthetic small molecule libraries for novel compounds affecting a broad range of plant processes. Along with this emphasis were methods necessary for successful screening campaigns including automation and imaging, cheminformatics, and protocols for examining hormones and metabolites using mass spectroscopy, NMR, and HPLC. All of these technologies enabled chemicalscreening.Targetidentificationandvalidationwerecriticalaswell,butonlyseveral chapterswereincludedasthisreflectedwheretheplantchemicalgenomicscommunitywas at the time. There were still relatively few examples in academia where small molecule protein targets were identified successfully. This has changed as the community of plant biologists utilizing small molecule approaches has increased along with increased sophisti- cationofscreeningandtargetproteinidentification. The field has now evolved to the point that finding a novel bioactive chemical and its cognate target is important or even required for scientific impact. For the basic research community,itiscriticalthat asmallmoleculeand itstarget(s)contributenewinsightsinto plant biology. At the time of the first edition, the primary means of target identification in plantswastheuseofArabidopsisgeneticsandgenomicsapproaches,primarilyforwardEMS and reverse genetic strategies. Yeast and other model systems were also employed. We termedthefieldchemicalgenomicsbecauseofthegenomicsemphasis.Todayitisprobably more encompassing to term our field as chemical biology because we utilize chemistry including synthetic (and native) small molecules and a variety of tools to understand biologicalprocesses. This latest volume contains some of the latest methods for the screening of plants for novel bioactive chemicals including areas not previously covered such as lipid signaling, a photoreceptor,andassayingdrugefficacyinplantcells.Inaddition,therearecontributions that highlight approaches that expand our vision of small molecule screens to include peptide ligands to generate new variation that can be exploited for discovery. An area of greatinterestinplantchemicalbiologythathasandcontinuestobeimportantisusingnovel chemicalstoaffectanddissecthormonesignalingasreflectedinchaptersonsmallmolecules impactingtheperceptionofthehormonesABA,ethylene,andauxin. Another recent development is the application of simpler microscale methods to sim- plify targetidentification and validation.This permits theuseofmorethanone methodto provide evidence of ligand-target interaction increasing confidence in our conclusions. We have emphasized these approaches with a section devoted to examples of these methods. Alongwiththesemicroscalemethodsareexamplesofchemicalproteomicsinwhichprote- omicsisusedtoidentifychemicaltargets.Itshouldbenotedthatthesemethodshavemostly been employed for target identification and validation in mammalian systems and are only now becoming more common practice in plants and thus reflected in the content of this volume. In addition, the emergence of sophisticated automated phenotyping and in vivo v vi Preface photoaffinity labeling combined with chemical proteomics is on the horizon for perhaps a futureeditionofthisseries. Plant Chemical Genomics: Methods and Protocols, Second Edition is an extension and companion to the first volume. We hope that both editions will provide a foundation in methodologies for novices to the field as well as experts within the plant chemical biology community. Riverside,CA,USA GlennR.Hicks WestLafayette,IN,USA ChunhuaZhang Contents Preface ..................................................................... v Contributors................................................................. ix PART I SCREENING FOR NOVEL SMALL MOLECULES 1 ChemicalGeneticstoUncoverMechanismsUnderlying Lipid-MediatedSignalingEventsinPlants ................................. 3 BibiRafeizaKhan,KentD.Chapman,andElisonB.Blancaflor 2 MethodforPhenotypicChemicalScreeningtoIdentify CryptochromeInhibitors ................................................ 17 EmikoOkubo-Kurihara,Wen-DeeOng,YukioKurihara, NatsumaroKutsuna,andMinamiMatsui 3 Whole-Seedling-BasedChemicalGeneticScreensinArabidopsis.............. 29 ShuaiHuangandXinLi 4 IdentificationofTypeIIISecretionInhibitorsforPlant DiseaseManagement.................................................... 39 RogerdePedroJove´,PauSebasti`a,andMarcValls 5 InvestigationofDrugEfficacybyScreeningBioactiveChemical EffectsonPlantCellSubcellularArchitecture .............................. 49 GianPietroDiSansebastiano PART II NEWAPPROACHES TO VARIATION: PEPTIDE SCREEN FOR NOVEL EFFECTORS 6 InVivoChemicalGenomicswithRandomCyclizedPeptides ................ 61 TautvydasShuipys,MaureenClancy,ElizabethEstrada-Johnson, andKevinM.Folta 7 InterferingPeptidesTargetingProtein–ProteinInteractions intheEthylenePlantHormoneSignalingPathwayasToolsto DelayPlantSenescence .................................................. 71 AlexanderHofmann,AlexanderMinges,andGeorgGroth PART III CHEMICAL GENOMICS IN HORMONE SIGNALING 8 TheScreeningforNovelInhibitorsofAuxin-InducedCa2+Signaling ......... 89 KjellDeVriese,LongNguyen,SimonStael,DominiqueAudenaert, TomBeeckman,andSteffenVanneste 9 IdentificationofABAReceptorAgonistsUsingaMultiplexed High-ThroughputChemicalScreening.................................... 99 JorgeLozano-Juste,IreneGarcı´a-Maquil(cid:1)on,Jose´Brea,Rocı´oPin˜a, ArmandoAlbert,PedroL.Rodriguez,andMarı´aIsabelLoza vii viii Contents 10 ALuciferaseReporterAssaytoIdentifyChemicalActivators ofABASignaling ....................................................... 113 IreneGarcı´a-Maquil(cid:1)on,PedroL.Rodriguez,AdityaS.Vaidya, andJorgeLozano-Juste 11 IdentificationofNovelMolecularRegulatorsModulating EthyleneBiosynthesisUsingEMS-BasedGeneticScreening.................. 123 ChanungPark,DongHyeSeo,JosephBuckley,andGyeongMeeYoon 12 InvestigationofAuxinBiosynthesisandActionUsingAuxin BiosynthesisInhibitors .................................................. 131 KazuoSoeno,AkikoSato,andYukihisaShimada PART IV TARGET IDENTIFICATION AND CONFIRMATION APPROACHES 13 TargetProfilingofanAnticancerDrugCurcuminbyan InSituChemicalProteomicsApproach.................................... 147 Dan-danLiu,ChangZou,JianbinZhang,PengGao,YongpingZhu, YuqingMeng,NanMa,MingLv,ChengchaoXu,QingsongLin, andJigangWang 14 Label-FreeTargetIdentificationandConfirmationUsing ThermalStabilityShiftAssays ............................................ 163 CeciliaRodriguez-FurlanandGlennR.Hicks 15 DrugAffinityResponsiveTargetStability(DARTS)Assayto DetectInteractionBetweenaPurifiedProteinandaSmallMolecule.......... 175 LeiHuang,DiwenWang,andChunhuaZhang 16 UsingDifferentialScanningFluorimetry(DSF)toDetect LigandBindingwithPurifiedProtein ..................................... 183 XiaohuiLiandChunhuaZhang 17 MicroscaleThermophoresis(MST)toDetecttheInteraction BetweenPurifiedProteinandSmallMolecule.............................. 187 LeiHuangandChunhuaZhang Index ...................................................................... 195 Contributors ARMANDOALBERT • InstitutodeQuı´micaFı´sicaRocasolano,ConsejoSuperiorde InvestigacionesCientı´ficas(IQFR-CSIC),Madrid,Spain DOMINIQUEAUDENAERT • ScreeningCore,VIB,Ghent,Belgium;CentreforBioassay DevelopmentandScreening(C-BIOS),GhentUniversity,Ghent,Belgium TOMBEECKMAN • DepartmentofPlantBiotechnologyandBioinformatics,GhentUniversity, Ghent,Belgium;VIBCenter forPlantSystemsBiology,Ghent,Belgium ELISONB.BLANCAFLOR • NobleResearchInstituteLLC,Ardmore,OK,USA JOSE´ BREA • InnopharmaScreeningPlatform,BioFarmaResearchGroup,Centrode Investigaci(cid:1)onenMedicinaMolecularyEnfermedadesCr(cid:1)onicas(CiMUS),Universidadde SantiagodeCompostela,SantiagodeCompostela,Spain JOSEPHBUCKLEY • DepartmentofBiologicalScience,PurdueUniversity,WestLafayette,IN, USA KENTD.CHAPMAN • DepartmentofBiologicalSciences,BioDiscoveryInstitute,Universityof NorthTexas,Denton,TX,USA MAUREEN CLANCY • HorticulturalSciencesDepartment,UniversityofFlorida,Gainesville, FL,USA ROGERDEPEDRO JOVE´ • DepartmentofGenetics,UniversityofBarcelona,Barcelona, Catalonia,Spain;CentreforResearchinAgriculturalGenomics(CSIC-IRTA-UAB- UB),Bellaterra,Catalonia,Spain KJELLDEVRIESE • DepartmentofPlantBiotechnologyandBioinformatics,Ghent University,Ghent,Belgium;VIBCenter forPlantSystemsBiology,Ghent,Belgium GIANPIETRODISANSEBASTIANO • DepartmentofBiologicalandEnvironmentalSciencesand Technologies(DiSTeBA),UniversityofSalento,Lecce,Italy ELIZABETHESTRADA-JOHNSON • HorticulturalSciencesDepartment,UniversityofFlorida, Gainesville,FL,USA KEVIN M.FOLTA • GeneticsandGenomicsGraduateProgram,UniversityofFlorida, Gainesville,FL,USA;HorticulturalSciencesDepartment,UniversityofFlorida, Gainesville,FL,USA;PlantMolecularandCellularBiologyProgram,Universityof Florida,Gainesville,FL,USA PENGGAO • InstituteofChineseMateriaMedica,andArtemisininResearchCenter,China AcademyofChineseMedicalSciences,Beijing,China IRENE GARCI´A-MAQUILO´N • InstitutodeBiologı´aMolecular yCelulardePlantas,Consejo SuperiordeInvestigacionesCientı´ficas,UniversidadPolite´cnicadeValencia(IBMCP- CSIC-UPV),Valencia,Spain GEORGGROTH • InstituteofBiochemicalPlantPhysiology,HeinrichHeineUniversity Du¨sseldorf,Du¨sseldorf,Germany GLENNR.HICKS • DepartmentofBotanyandPlantSciences,InstituteofIntegrative GenomeBiology,UniversityofCalifornia,Riverside,CA,USA;UppsalaBioCenter, SwedishUniversityofAgriculturalSciences,Uppsala,Sweden ALEXANDERHOFMANN • InstituteofBiochemicalPlantPhysiology,HeinrichHeineUniversity Du¨sseldorf,Du¨sseldorf,Germany LEIHUANG • DepartmentofBotanyandPathology,PurdueUniversity,WestLafayette,IN, USA;Center forPlantBiology,PurdueUniversity,WestLafayette,IN,USA ix
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