This page intentionally left blank P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 MICROBIAL BIOTECHNOLOGY Knowledgeinmicrobiologyisgrowingexponentiallythroughthedetermination ofgenomicsequencesofhundredsofmicroorganismsandtheinventionofnew technologies,suchasgenomics,transcriptomics,andproteomics,todealwith thisavalancheofinformation. Thesegenomicdataarenowexploitedinthousandsofapplications,rang- ingfrommedicine,agriculture,organicchemistry,publichealth,andbiomass conversion,tobiomining.MicrobialBiotechnologyfocusesonusesofmajorsoci- etalimportance,enablinganin-depthanalysisofthesecriticallyimportantappli- cations.Some,suchaswastewatertreatment,havechangedonlymodestlyover time;others,suchasdirectedmolecularevolution,or“green”chemistry,areas currentastoday’sheadlines. Thisfullyrevisedsecondeditionprovidesanexcitinginterdisciplinaryjourney throughtherapidlychanginglandscapeofdiscoveryinmicrobialbiotechnology. Anidealtextforcoursesinappliedmicrobiologyandbiotechnology,thisbook willalsoserveasaninvaluableoverviewofrecentadvancesinthisfieldforpro- fessionallifescientistsandforthediversecommunityofotherprofessionalswith interestsinbiotechnology. AlexanderN.Glazerisabiochemistandmolecularbiologistandhasbeenonthe facultyoftheUniversityofCaliforniasince1964.HeisaProfessoroftheGraduate SchoolintheDepartmentofMolecularandCellBiologyattheUniversityofCali- fornia,Berkeley.Dr.GlazerisamemberoftheNationalAcademyofSciencesand aFellowoftheAmericanAcademyofArtsandSciences,theAmericanAcademy ofMicrobiology,theAmericanAssociationfortheAdvancementofScience,and theCaliforniaAcademyofSciences.HewastwicetherecipientofaGuggenheim Fellowship.HewastherecipientoftheBotanicalSocietyofAmericaDarbaker Prize, 1980 and the National Academy of Sciences Scientific Reviewing Prize, 1991, a lecturer of the Foundation for Microbiology, 1996–98; and a National GuestLecturer,NewZealandInstituteofChemistry,1999.Dr.Glazerhasauthored over250researchpapersandreviews.Heisaco-inventoronmorethan40U.S. patents.Since1996,hehasservedasamemberoftheEditorialAffairsCommittee ofAnnualReviews,Inc. HiroshiNikaidoisabiochemistandmicrobiologist.HereceivedhisM.D.from KeioUniversityinJapanin1955andbecameafacultymemberatHarvardMed- icalSchoolin1963,beforemovingtoUniversityofCaliforniain1969.Heisa ProfessorofBiochemistryandMolecularBiologyintheDepartmentofMolecu- larandCellBiologyattheUniversityofCalifornia,Berkeley.Dr.NikaidoisaFellow oftheAmericanAcademyofArtsandSciencesandtheAmericanAcademyof Microbiology. He was the recipient of a Guggenheim Fellowship, NIH Senior InternationalFellowship,PaulEhrlichprize(1969),Hoechst-RousselAwardof AmericanSocietyforMicrobiology(1984),andFreedom-to-DiscoverAwardfor DistinguishedResearchinInfectiousDiseasesfromBristol-MyersSquibb(2004). HewasanEditorofJournalofBacteriologyfrom1998to2002.Dr.Nikaidohas authorednearly300researchpapersandreviews. i P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 MICROBIAL BIOTECHNOLOGY Knowledgeinmicrobiologyisgrowingexponentiallythroughthedetermination ofgenomicsequencesofhundredsofmicroorganismsandtheinventionofnew technologies,suchasgenomics,transcriptomics,andproteomics,todealwith thisavalancheofinformation. Thesegenomicdataarenowexploitedinthousandsofapplications,rang- ingfrommedicine,agriculture,organicchemistry,publichealth,andbiomass conversion,tobiomining.MicrobialBiotechnologyfocusesonusesofmajorsoci- etalimportance,enablinganin-depthanalysisofthesecriticallyimportantappli- cations.Some,suchaswastewatertreatment,havechangedonlymodestlyover time;others,suchasdirectedmolecularevolution,or“green”chemistry,areas currentastoday’sheadlines. Thisfullyrevisedsecondeditionprovidesanexcitinginterdisciplinaryjourney throughtherapidlychanginglandscapeofdiscoveryinmicrobialbiotechnology. Anidealtextforcoursesinappliedmicrobiologyandbiotechnology,thisbook willalsoserveasaninvaluableoverviewofrecentadvancesinthisfieldforpro- fessionallifescientistsandforthediversecommunityofotherprofessionalswith interestsinbiotechnology. AlexanderN.Glazerisabiochemistandmolecularbiologistandhasbeenonthe facultyoftheUniversityofCaliforniasince1964.HeisaProfessoroftheGraduate SchoolintheDepartmentofMolecularandCellBiologyattheUniversityofCali- fornia,Berkeley.Dr.GlazerisamemberoftheNationalAcademyofSciencesand aFellowoftheAmericanAcademyofArtsandSciences,theAmericanAcademy ofMicrobiology,theAmericanAssociationfortheAdvancementofScience,and theCaliforniaAcademyofSciences.HewastwicetherecipientofaGuggenheim Fellowship.HewastherecipientoftheBotanicalSocietyofAmericaDarbaker Prize, 1980 and the National Academy of Sciences Scientific Reviewing Prize, 1991, a lecturer of the Foundation for Microbiology, 1996–98; and a National GuestLecturer,NewZealandInstituteofChemistry,1999.Dr.Glazerhasauthored over250researchpapersandreviews.Heisaco-inventoronmorethan40U.S. patents.Since1996,hehasservedasamemberoftheEditorialAffairsCommittee ofAnnualReviews,Inc. HiroshiNikaidoisabiochemistandmicrobiologist.HereceivedhisM.D.from KeioUniversityinJapanin1955andbecameafacultymemberatHarvardMed- icalSchoolin1963,beforemovingtoUniversityofCaliforniain1969.Heisa ProfessorofBiochemistryandMolecularBiologyintheDepartmentofMolecu- larandCellBiologyattheUniversityofCalifornia,Berkeley.Dr.NikaidoisaFellow oftheAmericanAcademyofArtsandSciencesandtheAmericanAcademyof Microbiology. He was the recipient of a Guggenheim Fellowship, NIH Senior InternationalFellowship,PaulEhrlichprize(1969),Hoechst-RousselAwardof AmericanSocietyforMicrobiology(1984),andFreedom-to-DiscoverAwardfor DistinguishedResearchinInfectiousDiseasesfromBristol-MyersSquibb(2004). HewasanEditorofJournalofBacteriologyfrom1998to2002.Dr.Nikaidohas authorednearly300researchpapersandreviews. i P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 MOLDS 1 Penicillium chrysogenum 2 2 Monascus purpurea 3 Penicillium notatum 4 Aspergillus niger 5 3 5 Aspergillus oryzae 1 4 YEASTS 1 Saccharomyces cerevisiae 3 4 2 Candida utilis 2 5 3 Aureobasidium pullulans 13 12 4 Trichosporon cutaneum 1 11 14 6 5 Saccharomycopsis capsularis 15 6 Saccharomycopsis lipolytica 10 7 7 Hanseniaspora guilliermondii 9 8 8 Hansenula capsulata 9 Saccharomyces carlsbergensis 10 Saccharomyces rouxii 11 Rhodotorula rubra 12 Phaffia rhodozyma 13 Cryptococcus laurentii 14 Metschnikowia pulcherrima 15 Rhodotorula pallida CulturesofmoldsandyeastsonnutrientagaringlassPetridishes.FromH.Phaff,Indus- trialmicroorganisms,ScientificAmerican,September1981.Copyright©1981byScientific American,Inc.Allrightsreserved. ii P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 MICROBIAL BIOTECHNOLOGY Fundamentals of Applied Microbiology, Second Edition Alexander N. Glazer UniversityofCalifornia,Berkeley Hiroshi Nikaido UniversityofCalifornia,Berkeley iii CAMBRIDGEUNIVERSITY PRESS Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo Cambridge University Press The Edinburgh Building, Cambridge CB2 8RU, UK Published in the United States of America by Cambridge University Press, New York www.cambridge.org Information on this title: www.cambridge.org/9780521842105 © Alexander N. Glazer and Hiroshi Nikaido 2007 This publication is in copyright. Subject to statutory exception and to the provision of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published in print format 2007 ISBN-13 978-0-511-34136-6 eBook (EBL) ISBN-10 0-511-34136-9 eBook (EBL) ISBN-13 978-0-521-84210-5 hardback ISBN-10 0-521-84210-7 hardback Cambridge University Press has no responsibility for the persistence or accuracy of urls for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 WededicatethisbooktoEvaandKishiko, forthegiftofyearsofsupport,tolerance,andpatience. v P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 vi P1:JZP 0521842107pre CUFX119/Glazer 0521842107 June21,2007 19:13 Contents in Brief Preamble page xiii Acknowledgments xvii 1 MicrobialDiversity 1 2 MicrobialBiotechnology:Scope,Techniques,Examples 45 3 ProductionofProteinsinBacteriaandYeast 90 4 TheWorldof“Omics”:Genomics,Transcriptomics, Proteomics,andMetabolomics 147 5 RecombinantandSyntheticVaccines 169 6 Plant–MicrobeInteractions 203 7 Bacillusthuringiensis(Bt)Toxins:MicrobialInsecticides 234 8 MicrobialPolysaccharidesandPolyesters 267 9 PrimaryMetabolites:OrganicAcidsandAminoAcids 299 10 SecondaryMetabolites:AntibioticsandMore 324 11 BiocatalysisinOrganicChemistry 398 12 Biomass 430 13 Ethanol 458 14 EnvironmentalApplications 487 Index 541 Advancesofparticularrelevanceandimportancewillbeposted periodicallyonthewebsitewww.cambridge.org/glazer. vii