Plant Secondary Metabolism Engineering: Methods and Applications PDF
Preview Plant Secondary Metabolism Engineering: Methods and Applications
M M B TM ETHODS IN OLECULAR IOLOGY SeriesEditor JohnM.Walker SchoolofLifeSciences UniversityofHertfordshire Hatfield,Hertfordshire,AL109AB,UK Forothertitlespublishedinthisseries,goto www.springer.com/series/7651 Plant Secondary Metabolism Engineering MethodsandApplications Editedby Arthur Germano Fett-Neto UniversidadeFederaldoRioGrandedoSul,PortoAlegre,RS,Brazil Editor ArthurGermanoFett-Neto UniversidadeFederaldo RioGrandedoSul CentrodeBiotecnologia PortoAlegre-RS Brazil [email protected] ISSN1064-3745 e-ISSN1940-6029 ISBN978-1-60761-722-8 e-ISBN978-1-60761-723-5 DOI10.1007/978-1-60761-723-5 SpringerNewYorkDordrechtHeidelbergLondon LibraryofCongressControlNumber:2010923085 ©SpringerScience+BusinessMedia,LLC2010 Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewrittenpermissionof thepublisher(HumanaPress,c/oSpringerScience+BusinessMedia,LLC,233SpringStreet,NewYork,NY10013, USA),exceptforbriefexcerptsinconnectionwithreviewsorscholarlyanalysis.Useinconnectionwithanyformof informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdevelopedisforbidden. Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,eveniftheyarenotidentified assuch,isnottobetakenasanexpressionofopinionastowhetherornottheyaresubjecttoproprietaryrights. Whiletheadviceandinformationinthisbookarebelievedtobetrueandaccurateatthedateofgoingtopress,neither theauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityforanyerrorsoromissionsthatmay bemade.Thepublishermakesnowarranty,expressorimplied,withrespecttothematerialcontainedherein. Cover illustration: Fruit-bearing shoots of the Brazilian Atlantic Forest understorey tree Psychotria brachyceras (Rubiaceae). This species accumulates an unusual monoterpene indole alkaloid, brachycerine, which is induced in response to wounding, UV-exposure, jasmonate application, drought and osmotic stress. Its function is probably relatedtoitscapacitytomitigatereactiveoxygenspecies,actingbothasantioxidantandantimutagenicagent. Printedonacid-freepaper HumanaPressispartofSpringerScience+BusinessMedia(www.springer.com) Preface As sessile organisms, plants have evolved an amazing array of metabolic pathways leading to molecules capable of responding promptly and effectively to stress situations imposed by biotic and abiotic factors. These pathways, often recruited during biological evolu- tion from essential primary metabolism pathways upon initial gene duplication, combine carbon, hydrogen, oxygen, nitrogen, and sulfur into molecules that are capable of herbi- vore deterrence, tri-trophic signaling (i.e., attracting herbivore predators and parasites), pathogen inhibition, integrating defense responses, UV absorption, quenching of reac- tive oxygen species, allelopathic activity, attracting pollinators, or seed dispersing animals, heat dissipation, among other activities. Throughout the kingdom Plantae, there are tens of thousands of molecules, frequently restricted to specific taxonomic groups, which play this major role of plant interaction with the environment and are extremely important for plant fitness; these are historically referred to as secondary metabolites, also known as naturalproducts. In spite of our detailed knowledge of only a fraction of plant secondary metabolic pathways, particularly when considering tropical and subtropical phytodiversity, some major patterns have emerged, revealing a complex regulation of this metabolism. Both constitutive and inducible secondary metabolism activity can be found in different plant species, and frequently an intermediate profile of metabolic activity between these two strategies can be found. A strict spatial and temporal control of gene expression ensures the correct accumulation pattern of various secondary products. Organ-specific, tissue- specific, and cell type-specific expression of different portions of a single metabolic path- way are not uncommon in the biosynthesis of alkaloids and terpenes, for example. The requiredtransportofmetabolicintermediatesconstitutesanadditionallevelofregulation. Within cells, different compartments participate in biosynthetic steps, including chloro- plasts, cytoplasm, endoplasmic reticulum, vacuoles, nucleus, and special structures, such as alkaloid vesicles. The induction of secondary metabolism gene expression by wound- ing, herbivore-derived molecules, pathogen elicitors, and oxidative stress caused by heat, drought, flooding, UV light, or temperature extremes is often mediated by integrating signaling molecules such as salicylic acid, jasmonic acid, and their derivatives. Ontogeny and circadian clock controlled expression are also important features of plant secondary metabolism. At the level of gene expression, the presence of master regulatory transcrip- tion factorsisacommon themein themetabolism ofphenolics,alkaloids, and glucosino- lates. These regulators are considered some of the best targets for engineering secondary metabolicpathways. As can be easily realized, effective engineering of plant secondary metabolism path- ways is not a trivial task, mostly due to the various levels of regulation and the often observed close dependence of subcellular, tissue, and organ differentiation for effective expression of metabolic steps. Nonetheless, examples of successful engineering of plants, plant cell cultures, and heterologous expression of plant secondary metabolism genes in microbes are available. The purpose of this book is to provide a source of detailed prac- tical information on some of the most important methods employed in the engineering v vi Preface of plant secondary metabolism pathways and in the acquisition of essential knowledge in performing this activity. Some examples in which the application of these methods has allowed significant advances in the major goal of tailoring plants or microorganisms to becomefactoriesofrelevantplantsecondarymetabolitesarehighlighted.Someemerging strategies for metabolic engineering, still incipiently used in secondary metabolism, are also described, pointing to future directions in the field. The book is intended to be a resourceful reference tool for researchers (molecular biologists, plant physiologists, bio- chemists, chemical engineers, agronomists) engaged in the challenging task of modifying some of the most intricate products of plant evolution. Hopefully, it will assist scientists’ efforts in the goal of sustainably supplying, in a fast changing planet, the ever growing needs of humankind for natural chemicals, such as pharmaceuticals, nutraceuticals, agro- chemicals,foodandchemicaladditives,biofuels,andbiomass. ArthurGermanoFett-Neto Contents Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix 1. PlantSecondaryMetabolismandChallengesinModifyingItsOperation: AnOverview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 NaílaCannesdoNascimentoandArthurGermanoFett-Neto 2. SuppressionSubtractiveHybridizationasaTooltoIdentifyAnthocyanin Metabolism-RelatedGenesinAppleSkin . . . . . . . . . . . . . . . . . . . . . 15 YusukeBanandTakayaMoriguchi 3. Identification of Regulatory Protein Genes Involved in Alkaloid BiosynthesisUsingaTransientRNAiSystem . . . . . . . . . . . . . . . . . . . 33 YasuyukiYamada,NobuhikoKato,YasuhisaKokabu,QingyunLuo, JosephGogoDubouzetandFumihikoSato 4. Site-Directed Mutagenesis and Saturation Mutagenesis for the Functional Study of Transcription Factors Involved inPlantSecondaryMetaboliteBiosynthesis . . . . . . . . . . . . . . . . . . . . 47 SitakantaPattanaik, JoshuaR.Werkman, QueKong, andLingYuan 5. Isolation of Proteins Binding to Promoter Elements of Alkaloid Metabolism-RelatedGenesUsingYeastOne-Hybrid . . . . . . . . . . . . . . . 59 DéboraVomEndtandGiancarloPasquali 6. Modulation of Carotenoid Accumulation in Transgenic Potato byInducingChromoplastFormationwithEnhancedSinkStrength . . . . . . . 77 JoyceVanEck,XiangjunZhou,ShanLu,andLiLi 7. Over-expressionofRate-LimitingEnzymestoImproveAlkaloidProductivity . . 95 TomoyaTakemura,Yit-laiChow,TakehikoTodokoro,TakuyaOkamoto, andFumihikoSato 8. Microbial Expression of Alkaloid Biosynthetic Enzymes forCharacterizationofTheirProperties . . . . . . . . . . . . . . . . . . . . . . 111 HiromichiMinami,NobuhiroIkezawa,andFumihikoSato 9. Producing a Recombinant Flavin-Containing Monooxygenase from Coffea arabica in Escherichia coli for Screening of Potential NaturalSubstrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 IgorCesarinoandPauloMazzafera 10. Efficient Production of Active Form Recombinant Cassava HydroxynitrileLyaseUsingEscherichiacoliinLow-TemperatureCulture . . . . 133 HisashiSemba,EitaIchige,TadayukiImanaka,HaruyukiAtomi, andHidekiAoyagi vii viii Contents 11. Introduction of the Early Pathway to Taxol Biosynthesis in Yeast by Means of Biosynthetic Gene Cluster Construction UsingSOE-PCRandHomologousRecombination . . . . . . . . . . . . . . . 145 PiaDahmandStefanJennewein 12. BiocatalyticSynthesisofTritium(3H)-LabelledTaxa-4(5),11(12)-diene, thePathwayCommittingPrecursoroftheTaxoidDiterpenoids . . . . . . . . . 165 HansSchmeerandStefanJennewein 13. USER Cloning and USER Fusion: The Ideal Cloning Techniques forSmallandBigLaboratories . . . . . . . . . . . . . . . . . . . . . . . . . . 185 HussamH.Nour-Eldin,FernandoGeu-Flores, andBarbaraA.Halkier 14. Enrichment of Carotenoids in Flaxseed by Introducing aBacterialPhytoeneSynthaseGene . . . . . . . . . . . . . . . . . . . . . . . . 201 MasakiFujisawaandNorihikoMisawa 15. Metabolic Engineering by Plastid Transformation asaStrategytoModulateIsoprenoidYieldinPlants . . . . . . . . . . . . . . . 213 TomohisaHasunuma,AkihikoKondo,andChikahiroMiyake 16. Engineering High Yields of Secondary Metabolites in Rubia Cell CulturesThroughTransformationwithRolGenes . . . . . . . . . . . . . . . . 229 VictorP.Bulgakov,YuriN.Shkryl,andGalinaN.Veremeichik 17. Flow Cytometric Methods to Investigate Culture Heterogeneities forPlantMetabolicEngineering . . . . . . . . . . . . . . . . . . . . . . . . . 243 VishalGaurav,MartinE.Kolewe,andSusanC.Roberts 18. Phenylpropanoid Biosynthesis in Leaves and Glandular Trichomes ofBasil(OcimumbasilicumL.) . . . . . . . . . . . . . . . . . . . . . . . . . . 263 CíceroDeschampsandJamesE.Simon 19. Fusion with Fluorescent Proteins for Subcellular Localization ofEnzymesInvolvedinPlantAlkaloidBiosynthesis . . . . . . . . . . . . . . . . 275 PatríciaDuarte,JohanMemelink,andMarianaSottomayor 20. ImmunohistochemicalLocalisationofaPutativeFlavonoidTransporter inGrapeBerries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291 ElisaPetrussa,EnricoBraidot,MarcoZancani,CarloPeresson, AlbertoBertolini,SoniaPatui,ValentinoCasolo,SabinaPassamonti, FrancescoMacrì,andAngeloVianello 21. ElectrogenicBromosulfaleinTransportinIsolatedMembraneVesicles: Implementation in Both Animal and Plant Preparations for the Study ofFlavonoidTransporters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307 SabinaPassamonti,FedericaTramer,ElisaPetrussa,EnricoBraidot, andAngeloVianello SubjectIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337 Contributors HIDEKI AOYAGI •GraduateSchoolofLifeandEnvironmentalSciences,Universityof Tsukuba,Ibaraki,Japan HARUYUKI ATOMI •DepartmentofSyntheticChemistryandBiologicalChemistry, GraduateSchoolofEngineering,KyotoUniversity,Kyoto,Japan YUSUKE BAN •GraduateSchoolofLifeandEnvironmentalSciences,Universityof Tsukuba,Tsukuba,Ibaraki,Japan ALBERTO BERTOLINI •DepartmentofPlantBiologyandProtection,SectionofPlant Biology,UdineUniversity,Udine,Italy ENRICO BRAIDOT •DepartmentofPlantBiologyandProtection,SectionofPlant Biology,UdineUniversity,Udine,Italy VICTOR P. BULGAKOV •BioengineeringGroup,InstituteofBiologyandSoilScience, FarEastBranchofRussianAcademyofSciences,Vladivostok,Russia VALENTINO CASOLO •DepartmentofPlantBiologyandProtection,SectionofPlant Biology,UdineUniversity,Udine,Italy IGOR CESARINO •DepartmentofPlantBiology,InstituteofBiology,StateUniversityof Campinas,Campinas,SP,Brazil YIT-LAI CHOW •DivisionofIntegratedLifeScience,GraduateSchoolofBiostudies, KyotoUniversity,Kyoto,Japan PIA DAHM •InstituteofOrganicChemistryandBiochemistry,TechnicalUniversityof Darmstadt,Darmstadt,Germany CÍCERO DESCHAMPS •DepartmentofAgronomy,FederalUniversityofParana, Curitiba,PR,Brazil PATRÍCIA DUARTE •IBMC-InstituteofCellularandMolecularBiology,Porto University,Porto,Portugal JOSEPH GOGO •BiotransformationTeam,ScionResearch,Rotorua,NewZealand JOYCE VAN ECK BOYCE •ThompsonInstituteforPlantResearch,CornellUniversity, Ithaca,NY,USA DÉBORA VOM ENDT •StateUniversityofRioGrandedoSul,NovoHamburgo,RS, Brazil ARTHUR GERMANO FETT-NETO •DepartmentofBotanyandPlantPhysiology Laboratory,CenterforBiotechnology,FederalUniversityofRioGrandedoSul,Porto Alegre,RS,Brazil ix
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