Natural Product Biosynthesis by Microorganisms and Plants, Part A PDF
Preview Natural Product Biosynthesis by Microorganisms and Plants, Part A
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON and MELVIN I. SIMON Division of Biology California Institute of Technology Pasadena, California Founding Editors SIDNEY P. COLOWICK and NATHAN O. KAPLAN AcademicPressisanimprintofElsevier 525BStreet,Suite1900,SanDiego,CA92101-4495,USA 225WymanStreet,Waltham,MA02451,USA TheBoulevard,LangfordLane,Kidlington,Oxford,OX51GB,UK 32,JamestownRoad,LondonNW17BY,UK Radarweg29,POBox211,1000AEAmsterdam,TheNetherlands Firstedition2012 Copyright©2012,ElsevierInc.AllRightsReserved. Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedin anyformorbyanymeanselectronic,mechanical,photocopying,recordingorotherwise withoutthepriorwrittenpermissionofthepublisher PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRights DepartmentinOxford,UK:phone(+44)(0)1865843830;fax(+44)(0)1865853333; email:permissions@elsevier.com.Alternativelyyoucansubmityourrequestonlineby visitingtheElsevierwebsiteathttp://elsevier.com/locate/permissions,andselecting ObtainingpermissiontouseElseviermaterial Notice Noresponsibilityisassumedbythepublisherforanyinjuryand/ordamagetopersonsor propertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseor operationofanymethods,products,instructionsorideascontainedinthematerialherein. Becauseofrapidadvancesinthemedicalsciences,inparticular,independentverificationof diagnosesanddrugdosagesshouldbemade ForinformationonallAcademicPresspublications visitourwebsiteatstore.elsevier.com ISBN:978-0-12-394290-6 ISSN:0076-6879 PrintedandboundinUnitedStatesofAmerica 12 13 14 15 11 10 9 8 7 6 5 4 3 2 1 CONTRIBUTORS IkuroAbe GraduateSchoolofPharmaceuticalSciences,TheUniversityofTokyo,Tokyo,Japan SayakaMasadaAtsumi DepartmentofBiologicalSciences,BrockUniversity,St.Catharines,Ontario,Canada SarahE.Bloch DepartmentofBiochemistry,MolecularBiologyandBiophysics,UniversityofMinnesota, St.Paul,Minnesota,USA DavidE.Cane DepartmentofChemistry,BoxH,BrownUniversity,Providence,RhodeIsland,USA XiuyinChen TheNewZealandInstituteforPlant&FoodResearchLimited,Auckland,NewZealand KatrinaCornish DepartmentofHorticultureandCropScience,andDepartmentofFood,Agriculturaland BiologicalEngineering,OhioAgriculturalResearchandDevelopmentCenter,TheOhio StateUniversity,Wooster,Ohio,USA TohruDairi GraduateSchoolofEngineering,HokkaidoUniversity,Hokkaido,Japan ThuThuyT.Dang DepartmentofBiologicalSciences,UniversityofCalgary,Calgary,Alberta,Canada VincenzoDeLuca DepartmentofBiologicalSciences,BrockUniversity,St.Catharines,Ontario,Canada MelissaDokarry DepartmentofMetabolicBiology,JohnInnesCentre,NorwichResearchPark,Norwich, UnitedKingdom PeterJ.Facchini DepartmentofBiologicalSciences,UniversityofCalgary,Calgary,Alberta,Canada ScottC.Farrow DepartmentofBiologicalSciences,UniversityofCalgary,Calgary,Alberta,Canada SimonaFlorea DepartmentofPlantPathology,UniversityofKentucky,Lexington,Kentucky,USA StevenR.Garrett DepartmentofMetabolicBiology,JohnInnesCentre,NorwichResearchPark,Norwich, UnitedKingdom SolA.Green TheNewZealandInstituteforPlant&FoodResearchLimited,Auckland,NewZealand xi xii Contributors BarbaraA.Halkier CenterforDynamicMolecularInteractions,DepartmentofPlantBiologyand Biotechnology,MolecularPlantBiology,FacultyofLifeSciences,Universityof Copenhagen,Thorvaldsensvej,FrederiksbergC,Copenhagen,Denmark HaruoIkeda LaboratoryofMicrobialEngineering,KitasatoInstituteforLifeSciences,Kitasato University,Kanagawa,Japan YoheiKatsuyama DepartmentofBiotechnology,GraduateSchoolofAgriculturalandLifeSciences, TheUniversityofTokyo,Bunkyo-ku,Tokyo,Japan CarolineLaurendon DepartmentofMetabolicBiology,JohnInnesCentre,NorwichResearchPark,Norwich, UnitedKingdom DylanLevac DepartmentofBiologicalSciences,BrockUniversity,St.Catharines,Ontario,Canada MortenE.Møldrup CenterforDynamicMolecularInteractions,DepartmentofPlantBiologyand Biotechnology,MolecularPlantBiology,FacultyofLifeSciences,Universityof Copenhagen,Thorvaldsensvej,FrederiksbergC,Copenhagen,Denmark AdamJ.Matich TheNewZealandInstituteforPlant&FoodResearchLimited,PalmerstonNorth,New Zealand HiroyukiMorita GraduateSchoolofPharmaceuticalSciences,TheUniversityofTokyo,Tokyo,Japan RichardJ.Morris DepartmentofComputationalandSystemsBiology,JohnInnesCentre,NorwichResearch Park,Norwich,UnitedKingdom JosephP.Noel HowardHughesMedicalInstitute,JackH.SkirballCenterforChemicalBiologyand Proteomics,TheSalkInstituteforBiologicalStudies,LaJolla,California,USA SarahE.O’Connor JohnInnesCentre,DepartmentofBiologicalChemistry,andSchoolofChemistry, TheUniversityofEastAnglia,NorwichResearchPark,Norwich,UnitedKingdom PaulE.O’Maille DepartmentofMetabolicBiology,JohnInnesCentre,andInstituteofFoodResearch, NorwichResearchPark,Norwich,UnitedKingdom YasuoOhnishi DepartmentofBiotechnology,GraduateSchoolofAgriculturalandLifeSciences, TheUniversityofTokyo,Bunkyo-ku,Tokyo,Japan Contributors xiii AkpevweOnoyovwi DepartmentofBiologicalSciences,UniversityofCalgary,Calgary,Alberta,Canada DanielG.Panaccione DivisionofPlant&SoilSciences,WestVirginiaUniversity,Morgantown,WestVirginia, USA RyanM.Peterson DivisionofPharmaceuticalSciences,UniversityofWisconsin-Madison,Madison, Wisconsin,andDepartmentofChemistry,TheScrippsResearchInstitute,Jupiter, Florida,USA KatyL.Ryan DivisionofPlant&SoilSciences,WestVirginiaUniversity,Morgantown,WestVirginia, USA VonnySalim DepartmentofBiologicalSciences,BrockUniversity,St.Catharines,Ontario,Canada BoSalomonsen CenterforDynamicMolecularInteractions,DepartmentofPlantBiologyand Biotechnology,MolecularPlantBiology,FacultyofLifeSciences,Universityof Copenhagen,Thorvaldsensvej,FrederiksbergC,Copenhagen,Denmark ChristopherL.Schardl DepartmentofPlantPathology,UniversityofKentucky,Lexington,Kentucky,USA ClaudiaSchmidt-Dannert DepartmentofBiochemistry,MolecularBiologyandBiophysics,UniversityofMinnesota, St.Paul,Minnesota,USA BenShen MicrobiologyDoctoralTrainingProgram;DivisionofPharmaceuticalSciences,University ofWisconsin-Madison,Madison,Wisconsin;DepartmentofChemistry;Departmentof MolecularTherapeutics;NaturalProductsLibraryInitiativeatTSRI,TheScrippsResearch Institute,Jupiter,Florida,USA MichaelJ.Smanski MicrobiologyDoctoralTrainingProgram,UniversityofWisconsin-Madison,Madison, Wisconsin,USA ToshiyukiWakimoto GraduateSchoolofPharmaceuticalSciences,TheUniversityofTokyo,Tokyo,Japan GraysonT.Wawrzyn DepartmentofBiochemistry,MolecularBiologyandBiophysics,UniversityofMinnesota, St.Paul,Minnesota,USA Jing-KeWeng HowardHughesMedicalInstitute,JackH.SkirballCenterforChemicalBiologyand Proteomics,TheSalkInstituteforBiologicalStudies,LaJolla,California,USA xiv Contributors WenshuangXie DepartmentofHorticultureandCropScience,OhioAgriculturalResearchand DevelopmentCenter,TheOhioStateUniversity,Wooster,Ohio,USA YuukiYamada LaboratoryofMicrobialEngineering,KitasatoInstituteforLifeSciences,Kitasato University,Kanagawa,Japan FangYu DepartmentofBiologicalSciences,BrockUniversity,St.Catharines,Ontario,Canada PREFACE In2009,IeditedtwovolumesofMethodsinEnzymology(Volumes458and 459)entitled“Complexenzymesinmicrobialnaturalproductbiosynthesis.” Theprojectwasmotivatedbytwomainfactors.Thefirstwasthedevelop- ment,overthepreviousfewyears,ofanoveltoolboxofpracticaltechniques forthestudyofnaturalproductbiosynthesis,involvingafusionofchemistry, genetics,enzymology,andstructuralstudies,therebybringingwithinreach an understanding of the “programming” of complex, multifunctional enzyme systems that had not been attainable previously and opening the possibilityofcreating“unnaturalnaturalproducts”bygeneticengineering. The second was the increasing need for novel bioactive natural products, especially antibiotics and anticancer drugs, and the new possibilities for addressing this need by carrying out “chemistry through genetics” and by studyingthegamutofpotentialnaturalproductsrevealedbythesequencing of microbial genomes. Three years later, these driving forces are still very much alive, hence the motivation to extend the project. As well as including overview articles, the two 2009 volumes covered manyofthehotspotsinpeptideandpolyketideresearch,plusaminocoumarin compoundsandsomeaspectsofcarbohydrate-basednaturalproducts.There- fore,themainemphasisthistimeisonchemicalclassesthatwerenotincluded inthepreviousvolumes,notablyterpenoidsandalkaloids,aswellasfurther coverage of peptides and inclusion of Type III polyketides, which did not makeitintothepreviousvolumes.Interestingtailoringreactions,whichoften givenaturalproductstheirbiologicalactivitybyaddingfunctionalgroupsto the carbon skeletons assembled by complex enzyme systems, are also included. Less obvious, in a series dedicated to enzymology, is the inclusion of sections dealing with the isolation and study of novel classes of organisms andoforganismsfromnovelhabitats.Otherchaptersdescribeheterologous pathwayexpressionandmethodsforwakingupsleepinggeneclusters.The reasoning is that getting hold of the enzymes is an essential prerequisite for theirstudy.Apartfromitsintrinsicscientificinterest,thisisagrowthareain relation to natural product discovery and is revealing an Aladdin’s cave of novel metabolism, much of it unexpressed under the conditions employed in traditional natural product screening campaigns. xv xvi Preface In contrast to the previous two-volume set, which was focused on microorganisms, this time I have widened the coverage to include plants. Plantshavelongbeenknowntoproduceanenormousnumberofimportant natural products, but study of their enzymology at the detailed molecular biologicallevellaggedbehindthatofmicrobialproducts,largelyfortechni- cal reasons. With the rise of plant genomics, made possible by the recent development of next-generation sequencing technologies and the analysis of transcriptomes by RNAseq, which together bring the large genomes of higher plants within reach, this deficiency has been redressed and there arenowmanyexamplesofpenetratinganalysisofplantmetabolites.Where appropriate,chaptersonmicrobialsystems—bothbacterialandfungal—are groupedwithchaptersonplantmetabolitessothatinterestingcomparisons can be made. In a further difference from last time, the main criterion for inclusion in the new volumes is good biochemical and/or genetic under- standing of a biosynthetic pathway, combined with interesting chemistry and/or unusual producing organisms. Thus, the choice is not confined to “complex enzymes” per se. Especiallyinthedescriptionsofmethodstostudyplantsystems,thereis overlapbetweenafewofthechapters,eveniftheydealwiththeanalysisof differentclassesofmetabolites.Ishouldliketoregardthisasastrengthrather than a defect in editing! These technologies are still developing, so having more than one set of protocols to explore may be helpful to those who wishtoextendthetechniquestoclassesofcompoundsthatarenotexplicitly covered in these volumes. Volume A opens with a major section on terpenoids. Members of this huge class of natural products are derived from five-carbon isoprene units, ranging in number from hemiterpenes with one unit, monoterpenes with two,sesquiterpeneswiththree,diterpeneswithfour,tetraterpeneswitheight, andpolyterpeneswithmany.Atonetimethoughttoberareorevenabsent fromprokaryotes,theyarenowknowntobeimportantinbacteriaaswellasin the eukaryotic fungi. Coverageof the terpenoids in Volume A reflects this wide distribution and importance, with eight chapters devoted to various aspectsofthestudyofterpenoidcompounds.Severalofthechaptersintroduce novel, cutting-edge technology. Appropriately for Methods in Enzymology, Chapter1describesnovelenzymology:thesteady-statekineticcharacteriza- tionofplantsesquiterpenesynthasesbygaschromatography-massspectrom- etry(GC-MS).Likewise,Chapter4representsafineexampleofenzymology, defining and describing the specialized polyterpenoid synthase that makes natural rubber. Other chapters in this section deal with the genetic Preface xvii engineeringofterpenoidsandtheirexpressioninheterologoushosts,while providingamineofinformationonthebiosynthesisoftheindividualcom- pounds,rangingfromfungalmycotoxinstobacterialmenaquinones. ThenextgroupofchaptersinVolumeAisdevotedtothealkaloidsand glucosinolates.Alkaloidsrepresentperhapsthelongestknowngroupofplant natural products. They are highly diverse in their structures and biological activities but are united by the presence of a basic nitrogen atom at some positioninthemolecule.Chapters9and10describetechniquesforthedis- coveryandanalysisofmonoterpene-derivedindolealkaloids,whichinclude the crucial antitumor Vinca alkaloids as well as several other classes of molecules with important medicinal uses, while Chapter 11 deals with the L-tyrosine-derived benzylisoquinoline alkaloids from opium poppy and related species, again compounds of extreme pharmacological interest, including morphine. Chapter 12 introduces the ergot alkaloids, classically associated with plants but actually made by the fungi that parasitize them, notably species of Claviceps, but now known to be made by a wider range of fungi. This section ends with a chapter on the amino acid-derived glucosinolates of plants, notable as beneficial dietary components found in brassicas, and their heterologous expression in Nicotiana and in yeast. Asmentionedabove,polyketidesynthasesdominatedthe2009volumes in this series, but did not include the Type III systems, best known for the biosynthesis of anthocyanin pigments in higher plants but responsible for a widerangeofotherimportantcompoundsandnowwellestablishedalsoas the producers of metabolites of microorganisms, both bacterial and fungal. They differ from the Type I and II synthases in consisting of small homodimeric proteins rather than large multifunctional enzymes with a multitudeofseparateactivesites,makingtheminsomewayseasiertostudy biochemically but more cryptic in their programming. Chapters 14–16 describe the analysis and manipulation of these important enzyme systems. Peptide-derived natural products are perhaps best known as being derivedbynonribosomalassembly-linemechanismsverydistinctfromthose depending on the ribosome. Several examples were covered in the 2009 volumes, along with a single class of compounds—the lantibiotics— resulting from ribosomal biosynthesis followed by extensive posttransla- tional modifications. Volume B opens with four further examples of ribosomally derived metabolites: the thiopeptide antibiotics produced by Streptomyces and Bacillus species, microviridin made by cyanobacteria, the plant cyclotides, and the cyclic peptide toxins of mushrooms, including theinfamousamatoxins.Thissectionendswithaspecialactivityofanovel xviii Preface nonribosomal peptide synthetase, the Pictet-Spengler mechanism involved in the biosynthesis of tetrahydroisoquinoline antitumor antibiotics. The next section of Volume B contains three chapters describing very diverseenzymology.TheP–Cbondsinphosphonateandphosphinatenat- ural products endow them with a high level of stability and the ability to mimicphosphateestersandcarboxylates,sotheirbiosynthesisisparticularly intriguing.TheradicalSAMenzymescarryoutremarkablechemicaltrans- formations by releasing an active radical via the cleavage of S-adenosyl-L- methionine; the second chapter in this section describes novel methods for their purification and characterization. The third chapter describes methods for probing the biosynthesis of novel high-carbon sugar nucleo- sides containing up to 11 contiguous carbons. Very often, natural product biosynthesis proceeds by the assembly of a core backbone—perhaps a polyketide, peptide, or terpene—followed by reactions that add functional groups that endow the molecules with their specificbiologicalactivities.VolumeBcontinueswithasectioncontaining nine chapters devoted to such important tailoring reactions. It begins with one of the most famous classes of tailoring enzymes, the heme-dependent cytochromes P450, followed by the less well known nonheme iron- dependentenzymes.Thencometwochaptersonthehalogenatingenzymes of microorganisms and plants, first those that introduce fluorine and then chlorinating andbrominating enzymes.Nextcomesprenylation,hererep- resentedbyfungalenzymesofthedimethylallyltryptophansuperfamily.This chapterrelatestothebiosynthesisofergotalkaloidsandsocouldhavebeen placed in the alkaloid section of Volume A but is included in the tailoring enzyme section of Volume B because of the widespread importance of prenylation in determining the biological activity of molecules. Acylation is another crucial tailoring step in conferring biological activity on natural products; the section includes a chapter on one of the most important classes of acylating enzymes of plants, the serine carboxypeptidase-like acyltransferases.Theactinomycete-derivedenediynesaresomeofthemost remarkablenaturalproductsbothstructurallyandfortheirextremecytotox- icity.Twochaptersinthissectionderivefromaspectsoftheirbiosynthesis, but they are included for the much wider applicability of the resulting enzymology. Chapter 15 deals with 4-methylideneimidazole-5-one (MIO)-containing aminomutases that catalyze b-amino acid formation, and Chapter 16 deals with tailoring enzymes acting on carrier-protein- tethered substrates, an approach that promises to open new vistas in the engineering of designer natural products. The section ends with a chapter
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