PLANT CHEMICAL GENOMICS : methods and protocols.

196 Pages·2020·6.511 MB·English

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
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School of Lifeand MedicalSciences,
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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
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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