Complex Enzymes in Microbial Natural Product Biosynthesis, Part A: Overview Articles and Peptides PDF
Preview Complex Enzymes in Microbial Natural Product Biosynthesis, Part A: Overview Articles and Peptides
METHODS IN ENZYMOLOGY Editors-in-Chief JOHN N. ABELSON MELVIN I. SIMON AND Division of Biology California Institute of Technology Pasadena, California, USA Founding Editors SIDNEY P. COLOWICK NATHAN O. KAPLAN AND AcademicPressisanimprintofElsevier 525BStreet,Suite1900,SanDiego,CA92101-4495,USA 30CorporateDrive,Suite400,Burlington,MA01803,USA 32JamestownRoad,LondonNW17BY,UK Firstedition2009 Copyright#2009,ElsevierInc.AllRightsReserved. Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedinany formorbyanymeanselectronic,mechanical,photocopying,recordingorotherwisewithoutthe priorwrittenpermissionofthepublisher PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRightsDepartment inOxford,UK:phone(+44)(0)1865843830;fax(+44)(0)1865853333;email:permissions@ elsevier.com.AlternativelyyoucansubmityourrequestonlinebyvisitingtheElsevierwebsiteat http://elsevier.com/locate/permissions,andselectingObtainingpermissiontouseElseviermaterial Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or propertyasamatterofproductsliability,negligenceorotherwise,orfromanyuseoroperation ofanymethods,products,instructionsorideascontainedinthematerialherein.Becauseofrapid advancesinthemedicalsciences,inparticular,independentverificationofdiagnosesanddrug dosagesshouldbemade ForinformationonallAcademicPresspublicationsvisitour websiteatelsevierdirect.com ISBN:978-0-12-374588-0 ISSN:0076-6879 PrintedandboundinUnitedStatesofAmerica 09 10 11 12 10 9 8 7 6 5 4 3 2 1 C ONTRIBUTORS KhaledAbou-Hadeed InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland AntonyN.Appleyard Novacta Biosystems Ltd, BioPark Hertfordshire, Welwyn Garden City, United Kingdom BrianO.Bachmann Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University,Nashville,Tennessee,USA RichardH.Baltz CubistPharmaceuticalsInc,Lexington,Massachusetts,USA AndreasBechthold Institut fu¨r Pharmazeutische Wissenschaften, Lehrstuhl fu¨r Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs-Universita¨t Freiburg, Freiburg, Germany MervynBibb Department of Molecular Microbiology, John Innes Centre, Norwich Research Park,ColneyLane,Norwich,UnitedKingdom MichaelD.Burkart DepartmentofChemistryandBiochemistry,UniversityofCalifornia,SanDiego, LaJolla,California,USA GregoryL.Challis DepartmentofChemistry,UniversityofWarwick,Coventry,UnitedKingdom LisaE.Cooper Departments of Chemistry and Biochemistry and the Howard Hughes Medical Institute,UniversityofIllinois,Urbana,Illinois,USA Jesu´sCorte´s Novacta Biosystems Ltd, BioPark Hertfordshire, Welwyn Garden City, United Kingdom MichaelJ.Dawson Novacta Biosystems Ltd, BioPark Hertfordshire, Welwyn Garden City, United Kingdom xiii xiv Contributors ArnoldL.Demain Research Institute for Scientists Emeriti (R.I.S.E.), Drew University, Madison, NewJersey,USA StefanoDonadio KtedoGenandNAICONS,ViaFantoli,Milano,Italy MohamedS.Donia DepartmentofMedicinalChemistry,UniversityofUtah,SaltLakeCity,Utah,USA L.-O.Essen Biochemistry-Department of Chemistry, Philipps-University Marburg, Marburg, Germany RonaldO.Garcia Department of Pharmaceutical Biotechnology, Saarland University, Saarbru¨cken, Germany NinaGeib InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland MarcoGottelt Department of Microbial Physiology, GBB, University of Groningen, Haren, TheNetherlands BertoltGust Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universita¨t Tu¨bingen,Tu¨bingen,Germany JohannesHa¨rle Institutfu¨rPharmazeutischeWissenschaften,Lehrstuhlfu¨rPharmazeutischeBiolo- gieundBiotechnologie,Albert-Ludwigs-Universita¨tFreiburg,Freiburg,Germany AndrewHesketh Department of Molecular Microbiology, John Innes Centre, Norwich Research Park,ColneyLane,Norwich,UnitedKingdom KinyaHotta DepartmentofBiologicalSciences,NationalUniversityofSingapore,Singapore Nai-HuaHsiao Department of Microbial Physiology, GBB, University of Groningen, Haren, TheNetherlands NadiaKadi DepartmentofChemistry,UniversityofWarwick,Coventry,UnitedKingdom DanielKrug Department of Pharmaceutical Biotechnology, Saarland University, Saarbru¨cken, Germany Contributors xv BoLi Departments of Chemistry and Biochemistry and the Howard Hughes Medical Institute,UniversityofIllinois,Urbana,Illinois,USA DongBoLi InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland PalomaLiras Biotechnological Institute INBIOTEC, Scientific Park of Leo´n, and A´rea de Microbiolog´ıa, Facultad de Ciencias Biolo´gicas y Ambientales, Universidad de Leo´n,Leo´n,Spain FelipeLombo´ Departamento de Biolog´ıa Funcional and Instituto Universitario de Oncolog´ıa delPrincipadodeAsturias(I.U.O.P.A),UniversidaddeOviedo,Oviedo,Spain M.A.Marahiel Biochemistry-Department of Chemistry, Philipps-University Marburg, Marburg, Germany FlaviaMarinelli Department of Biotechnology and Molecular Sciences, University of Insubria, Varese,Italy NancyL.McKenzie Michael G. DeGroote Centre for Infectious Disease Research, Department of BiochemistryandBiomedicalSciences,McMasterUniversity,Hamilton,Ontario, Canada CarmenMe´ndez DepartamentodeBiolog´ıaFuncionalandInstitutoUniversitariodeOncolog´ıadel PrincipadodeAsturias(I.U.O.P.A),UniversidaddeOviedo,Oviedo,Spain JordanL.Meier DepartmentofChemistryandBiochemistry,UniversityofCalifornia,SanDiego, LaJolla,California,USA JasonMicklefield School of Chemistry and Manchester Interdisciplinary Biocentre, The University ofManchester,Manchester,UnitedKingdom PaoloMonciardini KtedoGen,ViaFantoli,Milano,Italy RolfMu¨ller Department of Pharmaceutical Biotechnology, Saarland University, Saarbru¨cken, Germany xvi Contributors JustinR.Nodwell Michael G. DeGroote Centre for Infectious Disease Research, Department of BiochemistryandBiomedicalSciences,McMasterUniversity,Hamilton,Ontario, Canada CarlosOlano DepartamentodeBiolog´ıaFuncionalandInstitutoUniversitariodeOncolog´ıadel PrincipadodeAsturias(I.U.O.P.A),UniversidaddeOviedo,Oviedo,Spain AlexP.Praseuth Department of Pharmacology and Pharmaceutical Sciences, University of SouthernCalifornia,LosAngeles,California,USA MikeB.Praseuth Department of Pharmacology and Pharmaceutical Sciences, University of SouthernCalifornia,LosAngeles,California,USA JacquesRavel Institute for Genomic Sciences, Department of Microbiology and Immunology, UniversityofMarylandSchoolofMedicine,Baltimore,Maryland,USA JohnA.Robinson InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland Jose´ A.Salas DepartamentodeBiolog´ıaFuncionalandInstitutoUniversitariodeOncolog´ıadel PrincipadodeAsturias(I.U.O.P.A),UniversidaddeOviedo,Oviedo,Spain EricW.Schmidt DepartmentofMedicinalChemistry,UniversityofUtah,SaltLakeCity,Utah,USA MargheritaSosio KtedoGen,ViaFantoli,Milano,Italy EviStegmann Institutfu¨rMikrobiologie,Mikrobiologie/Biotechnologie,Universita¨tTu¨bingen, Tu¨bingen,Germany RoderichD.Su¨ssmuth Institutfu¨rChemie,TechnischeUniversita¨tBerlin,Berlin,Germany MuratSunbul DepartmentofChemistry,TheUniversityofChicago,Chicago,Illinois,USA ErikoTakano Department of Microbial Physiology, GBB, University of Groningen, Haren, TheNetherlands Contributors xvii WilfredA.vanderDonk Departments of Chemistry and Biochemistry and the Howard Hughes Medical Institute,UniversityofIllinois,Urbana,Illinois,USA GillesP.vanWezel Molecular Genetics, Leiden Institute of Chemistry, Gorlaeus Laboratories, TheNetherlands KenjiWatanabe ResearchCoreforInterdisciplinarySciences,OkayamaUniversity,Okayama,Japan BarrieWilkinson Biotica,ChesterfordResearchPark,LittleChesterford,Essex,UnitedKingdom WolfgangWohlleben Institutfu¨rMikrobiologie,Mikrobiologie/Biotechnologie,Universita¨tTu¨bingen, Tu¨bingen,Germany KatharinaWoithe InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland JunYin DepartmentofChemistry,TheUniversityofChicago,Chicago,Illinois,USA KatjaZerbe InstituteofOrganicChemistry,UniversityofZu¨rich,Zu¨rich,Switzerland KeyaZhang DepartmentofChemistry,TheUniversityofChicago,Chicago,Illinois,USA P REFACE The complex structures of microbial natural products have fascinated chemists for decades. As the tools of chemistry and biochemistry were sharpened, huge advances in understanding natural product biosynthesis were made, but there were still barriers to a satisfactory understanding. Many such impediments were due to the instability of intermediates in thebiosyntheticpathways,whichhamperedchemicalanalysis.Atthesame time, a frequent inability to obtain active cell-free preparations severely limited the success of biochemical approaches. A striking example of these limitations is provided by the polyketides, the largest and most important family of secondary metabolites. Chemistry and biochemistry had deduced the relationships between polyketide and fatty acid biosynthesis and had revealedthebasicbiochemicalreactionsinvolved,buttherewaslittleunder- standing of the ‘‘programming’’ of the enzymes, that is control of the variables that make the polyketides such a varied class of chemicals: choice of starter and extender units for carbon chain building, and control of chain length, degree of reduction of keto groups, and chirality of carbon and hydroxyl branches. Isolation of the actinomycete gene clusters that encode the polyketide synthases, their sequencing, and their manipulation into unnatural combinations in the early 1990s changed the landscape almost overnight. There followed a period in which genetics provided a primary stimulus to much of the research in natural product biosynthesis. Now, chemistry, genetics, enzymology, and structural studies are working synergistically to reveal the details of biochemical control. Thistwo-volumesetofMethodsinEnzymologyreflectsthesedevelopments in the study of natural product biosynthesis. As expressed by Mel Simon in his invitation to edit the set, it is especially timely in view of the increasing need for novel bioactive natural products, especially antibiotics and anti- cancer drugs, and the new possibilities for addressing this need by carrying out ‘‘chemistry through genetics’’ and by studying the gamut of potential naturalproductsrevealedbythesequencingofmicrobialgenomes. WebeginVolumeAwiththeisolationandscreeningofvariouskindsof microorganisms, to provide the raw material for subsequent fundamental studiesorforthedevelopmentofnaturalproductsasdrugs.Thencomethree chaptersdealingwiththeregulationofsecondarymetaboliteproductionin actinomycetes – the group of filamentous soil bacteria that are preeminent secondarymetaboliteproducers–andhowanunderstandingofsuchregu- lation can furnish compounds that would otherwise be hard to obtain. xix xx Preface Nextarechapterscoveringthecloningandanalysisofbiosyntheticpathway genes and computer-based methods for predicting the products encoded by gene sets for two key classes of secondary metabolites, the polyketides and nonribosomal peptides, from DNA sequence data, as well as articles describing innovative approaches to probing their biosynthesis. Two final chapters in the first section deal with the biosynthesis of sugars and their attachmenttosecondarymetaboliteaglycones,therebyconferringbiological activity. The section on peptide natural products begins with an overview of nonribosomal peptide biosynthesis, followed by a detailed description of methods for studying the biosynthesis of the amino acids and other pre- cursorsthatfunctionasbuildingblocksintheirassembly,aswellasachapter on the heterologous expression of nonribosomal peptide synthetase genes. Next come chapters on a specific class of compounds in this super-family, the cephem beta-lactams, on a special type of iron-chelating siderophore, and on the important glycopeptide and lipopeptide families of antibiotics. Moving to ribosomally synthesised peptide natural products, two chapters cover the lantibiotics, a topic of increasing current focus in the search for antibiotics effective against resistant pathogens. We end Volume B with anotherexampleofribosomallysynthesisedpeptides,thistimecoupledwith techniques for metagenomics mining. Volume B is dominated by the polyketides, reflecting their pre- eminence as natural products. Kira Weissman introduces polyketide synthesis and the different types of polyketide synthases, and puts the 16 chapters in this section elegantly into context, making redundant any further remarks here, except to note the absence of a chapter on the type III polyketide synthases, an omission stemming from the last-minute withdrawal of the author chosen for this topic. The section on aminocou- marinscontainsasinglechapterthatprovidesaparticularlyfineexampleof the application of molecular genetics to another class of compounds, with considerable potential for the generation of ‘‘unnatural natural products’’ by genetic engineering techniques first developed for the polyketides. The volume ends with a section on carbohydrate-type natural products, with two chapters on aminoglycosides and one on the biosynthesis of the TDP-deoxysugars that play such a crucial role in conferring biological activity on a whole range of secondary metabolites, harking back to the chapters on sugar biosynthesis in Volume A. Inevitably,thechoiceoftopicstoincludeinthesevolumesissomewhat arbitrary. The peptides and polyketides chose themselves because of their importance amongst natural products,especially as antibiotics, and because of the huge amount of recent research devoted to them. Historically, the aminoglycosideswerecentre-stageintheearlydaysofantibioticdiscovery– streptomycin was the first important actinomycete antibiotic to be described, and only the second, after penicillin, from any source to be a Preface xxi medicalmarvel–andtheyprobablystillmakeupthethirdlargestchemical family of antibiotics, earning them a place in Volume B. Several other classesofmicrobialnaturalproductswerecontendersforinclusion:amino- coumarins, terpenoids, and tetrapyrroles amongst others. However, space constraints precluded inclusion of all of them, and in the end only the aminocoumarins made the cut. Hopefully, other classes will take their place in a further volume in due course, along with a fuller coverage of natural product production by a wider range of microorganisms outside of the actinomycetes. I am most grateful for the enthusiastic response that greeted my invitations to contribute to this project. Inevitably, leaders in the field have many calls on their time, but it was most gratifying that nearly all my invitees either accepted or offered suggestions for alternative authors. I am especially grateful to Greg Challis, Chaitan Khosla, Tom Simpson, and Chris Walsh for their insightful ideas. To those who accepted – as well as tothemanyco-authorswhowererecruitedtothewriting–thankyoufor thetimeandeffortthatwentintothepreparationofthechaptersandtothe friendly way in which you all responded to my – usually minor – editorial suggestions, making my task a very pleasant one. DAVID A. HOPWOOD
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