Handbook of fungal biotechnology, Volume 20 PDF
Preview Handbook of fungal biotechnology, Volume 20
Handbook of Fu ng a I Bi o te c hn o Io gy Second Edition, Revised and Expanded edited by Dilip K. Arora National Bureau of Agriculturally Important Microorganisms New Delhi, India Asso ciat e Editors Paul D. Bridge British Antarctic Survey Cambridge, United Kingdom Deepak Bhatnagar US.D epartment of Agriculture New Orleans, Louisiana, U.S.A. MARCEL MARCELD EKKERIN, C. NEWY ORK BASEL DEKKER © 2004 by Marcel Dekker, Inc. Althoughgreatcarehasbeentakentoprovideaccurateandcurrentinformation,neithertheauthor(s)northepublisher,noranyoneelse associatedwiththispublication,shallbeliableforanyloss,damage,orliabilitydirectlyorindirectlycausedorallegedtobecausedby thisbook.Thematerialcontainedhereinisnotintendedtoprovidespecificadviceorrecommendationsforanyspecificsituation. Trademarknotice:Productorcorporatenamesmaybetrademarksorregisteredtrademarksandareusedonlyforidentificationand explanationwithoutintenttoinfringe. LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress. ISBN:0-8247-4018-1 Thisbookisprintedonacid-freepaper. Headquarters MarcelDekker,Inc.,270MadisonAvenue,NewYork,NY10016,U.S.A. tel:212-696-9000;fax:212-685-4540 DistributionandCustomerService MarcelDekker,Inc.,CimarronRoad,Monticello,NewYork12701,U.S.A. tel:800-228-1160;fax:845-796-1772 EasternHemisphereDistribution MarcelDekkerAG,Hutgasse4,Postfach812,CH-4001Basel,Switzerland tel:41-61-260-6300;fax:41-61-260-6333 WorldWideWeb http://www.dekker.com Thepublisheroffersdiscountsonthisbookwhenorderedinbulkquantities.Formoreinformation,writetoSpecialSales/Professional Marketingattheheadquartersaddressabove. Copyrightq2004byMarcelDekker,Inc.AllRightsReserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying,microfilming,andrecording,orbyanyinformationstorageandretrievalsystem,withoutpermissioninwritingfromthe publisher. Currentprinting(lastdigit): 10 9 8 7 6 5 4 3 2 1 PRINTEDINTHEUNITEDSTATESOFAMERICA © 2004 by Marcel Dekker, Inc. MYCOLOGY SERIES Editor J. W. Bennett Professor Department of Cell and Molecular Biology Tulane University New Orleans, Louisiana Founding Editor Paul A. Lemke 1. Viruses and Plasmids in Fungi, edited by Paul A. Lemke 2. The Fungal Community: Its Organization and Role in the Ecosystem, edited by Donald T. Wicklow and George C. Carroll 3. Fungi Pathogenic for Humans and Animals (in three parts), edited by Dexter H. Howard 4. Fungal Differentiation:A Contemporary Synthesis, edited by John E. Smith 5. Secondary Metabolism and Differentiation in Fungi, edited by Joan W. Bennett and Alex Ciegler 6. Fungal Protoplasts, edited by John F. Peberdy and Lajos Ferenczy 7. Viruses of Fungi and Simple Eukaryotes, edited by Yigal Koltin and Michael J. Leibowitz 8. Molecular Industrial Mycology: Systems and Applications for Filamentous Fungi, edited by Sally A. Leong and Randy M. Berka 9. The Fungal Community: Its Organization and Role in the Ecosystem, Second Edition, edited by George C. Carroll and Donald T. Wicklow 10. Stress Tolerance of Fungi, edited by D. H. Jennings 11. Metal lons in Fungi, edited by Gunther Winkelmann and Dennis R. Winge 12. Anaerobic Fungi: Biology, Ecology, and Function, edited by Douglas 0. Mountfort and Colin G. Orpin 13. Fungal Genetics: Principles and Practice, edited by Cees J. Bos 14. Fungal Pathogenesis: Principles and Clinical Applications, edited by Richard A. Calderone and Ronald L. Cihlar 15. Molecular Biology of Fungal Development, edited by Heinz D. Osiewacz 16. Pathogenic Fungi in Humans and Animals: Second Edition, edited by Dexter H. Howard 17. Fungi in Ecosystem Processes, John Dighton 18. Genomics of Plants and Fungi, edited by Rolf A. Prade and Hans J. Bohnert 19 . Clavicipitalean Fungi: Evolutionary Biology, Chemistry, Biocontrol, and Cultural Impacts, edited by James F. White Jr., Charles W. Bacon, Nigel L. Hywel-Jones, and Joseph W. Spatafora 20. Handbook of Fungal Biotechnology, Second Edition, edited by Dilip K. Arora 21 . Fungal Biotechnology in Agricultural, Food, and EnvironmentalA pplications, edited by Dilip K. Arora Additional Volumes in Preparation Handbook of lndustrial Mycology, edited by Zhiqiang An © 2004 by Marcel Dekker, Inc. Preface The fungal kingdom comprises one of the most diverse groups of living organisms. They are numerous, ubiquitous, and undertakemanyroles,bothindependentlyandinassociationwithotherorganisms.Thefungalspeciesrangefromthosethe sizeofafewmicrometersuptolargerfungiwithfruitingbodiesrangingfromseveralcentimeterstometers,andinextreme cases they can develop into a colonial organism that covers many hectares. This diversity of form is also mirrored by functionaldiversityasfungicanvirtuallyoccupyallecologicalniches,fromslow-growingendolithiccommunitiesinthe polar regions to highly specialized plant and animal pathogens, and rapid degraders of organic materials in tropical environments. The span of functional diversity in fungi makes them the richest model system in cell biology. Recent developmentsinmolecularbiologytechniques,includingDNAamplification,cloningandexpressionsystems,andmodern genomic and proteomic analyses have yielded the discovery of new compounds, and also offered tools to investigate, characterize, and exploit both new and long established fungal activities. Fungi have played a significant role in several biotechnology-basedindustrialprocessesandtheformulationofavarietyofcompounds.Fungiarealsothetargetofmany biotechnologicalapplications,fromthedevelopmentandproductionofnoteworthypharmaceuticalsandindustrialproducts totheir useassystems for homologous andheterologous gene overexpression. Thebulkofavailableliteraturecoversallthemajoraspectsofgeneralmycology,muchofwhichisthemedintobroad subjectareassuchassystematics,ecology,biochemistry,pathology,andmolecularbiology.However,thereisascarcityof compiled literature related strictly to the basic principles of applied mycology and fungal biotechnology. Their broader implicationsinpublishedliteraturearefragmentedoverseveralspecializedjournals.Inordertoattempttobringtogether suchadiversefield,I,alongwithcoeditors,venturedtoeditthefive-volumeseriesHandbookofAppliedMycologyin1992. Thisseriesofferedacomprehensivetreatmentofbasicprinciples,methods,andapplicationsofmycologyasanintegrated andmultidisciplinarysubject.Thesefivevolumespresentedandcollatedthemajoraspectsofappliedmycologyandserved as the standard reference for students, teachers, and researchers. Since 1992, significant developments in both biological sciencesandindustryhavebroadenedtheconceptualbasisoffungalecology,physiology,andbiochemicalprocessesthat aredirectlyrelevanttobiotechnologicalusageandmanipulation.AsaresultitseemedtimelytorevisetheoriginalVolume 4 (Fungal Biotechnology) and to review the current developments and highlight advances in rapidly expanding areas of molecular technologies inindustry,commercial production technology, andmedical biotechnology. The revised second edition of the Handbook of Fungal Biotechnology is intended to provide a broad and detailed introductiontothedifferentaspectsoffungalbiotechnology,withchapterscoveringmoleculartechnologies,commercial fungal applications, medical mycology, culture collections, legal aspects, and biosafety. The contributions include both reviewsofexistingfungalbiotechnologyapplicationsanddetailsofnewprocessesthatmaybecomemajorapplicationsin the future. For example, new chapters address topics ranging from cell biology of hyphae, protoplast fusion, metabolic regulation pathways, nuclei and chromosomes to genomics, gene clustering, gene cloning and sequencing, fungal mitochondrial genome, fungal genome and evolution, the role of GPF in fungal biotechnology, and DNA chips and © 2004 by Marcel Dekker, Inc. microarrays. Coverage has been expanded on commercial applications of fungi, such as the application of genetic engineering for strain improvement, genetic importance of wine yeasts, fungi in brewing, alcohol production, fungal enzymes,roleofchitin,polysaccharides,lipidsinfungalbiotechnology,productionofcitricacids,caretenoids,terpenoids, antibiotics, antifungal drugs, and antitumor and immunomodulatory compounds. Chapters that have direct or indirect significance inmedical biotechnology have also been added. Thevastarrayofusageandpropertiesistestimonytothecountlesswaysinwhichmankindcanharnessthebenefitof fungi; therefore, characterization techniques and methods of preservations of fungi, the recent development in biotechnology and intellectual property, access to genetic resources, and benefit sharing is essential. These challenging areasoffungalbiotechnologyarealsocoveredinthisbook.Potentialbenefitsanddangersofgeneticallymodifiedfoodsand mycoherbicidesareevaluated.Therefore,theaimofthishandbookistoprovideasnapshotintimeastotheuseoffungal biotechnology indifferent key areas, and toidentifypotential directions andpossibilities for the future. Thesubjectareasrelatedtoagriculture,food,andenvironmentalbiotechnologyarecoverednotinthisvolumebutinthe simultaneously published Fungal Biotechnology in Agricultural, Food, and Environmental Applications from the same editor. In assembling this volume, I have collaborated with world-renowned scientists to illustrate many application areas of fungalbiotechnology,frombothindustryandacademia.Thecontributorsarefromabroadinternationalbackground,and thusreflectthediverseactivitiesoccurringworldwide.Irecognizeseriousdifficultiesindevelopingacomprehensivebook onfungalbiotechnologybecauseoftherangeandcomplexityoftheemergingknowledge.However,wehaveattemptedto bring together pertinent information that may serve the needs of the reader, as a quick reference to a subject that might otherwisebedifficulttolocate,andbyfurnishingastartingpointforfurtherstudy.Ihopethatthecomprehensionofthis materialbyreaderswillenhancetheirunderstandingandhelpthemtogainnewappreciationformanypotentialbenefitsof fungal biotechnology in a wide variety of fields. The book should be of great interest not only to students, teachers, and researchers but also to agricultural practitioners, mycologists, botanists, microbiologists, molecular biologists, food scientists, biochemists, ecologists, genetic engineers, environmental scientists, pharmacologists, and all those concerned with issues related tosignificant developments inthe field offungalbiotechnology. Iamgratefultomanycolleaguesfordiscussionsandtheiradviceduringthepreparationofthisedition,andtheacademic nicheoftheBanarasHinduUniversityfortheopportunitytocompletethisgreattask.Iamgratefultomanyinternational authorities and specialists who have graciously consented to share their perspectives and expertise on the diverse applicationsof fungalbiotechnology, andcontributed chapters. IamalsoindebtedtoMs.Sandra Beberman,VicePresident,MarcelDekker, Inc.,andMs.DanaBigelow,Production Editor, for their skill, patience,encouragement,guidance, and support. DilipK. Arora © 2004 by Marcel Dekker, Inc. Contents Preface Contributors I CELL BIOLOGY, BIOCHEMICAL AND MOLECULAR TECHNOLOGIES 1CellBiologyofHyphae Oded Yarden 2ProtoplastIsolation,Regeneration,andFusioninFilamentousFungi ShubhaP. Kale andDeepakBhatnagar 3MetabolicPathwayRegulation Perng-Kuang Chang and RichardB. Todd 4FungalNucleiandChromosomes Benjamin C. K.Lu 5GenomicsofFilamentousFungi:AGeneralReview AhmadM. Fakhouryand Gary A.Payne 6StabilityandInstabilityofFungalGenomes A. JohnClutterbuck 7SecondaryMetabolicGeneClustersinFilamentousFungi Jeffrey W.Cary 8ApplicationofGeneCloninginFungalBiotechnology La(cid:1)szlo(cid:1) Hornok andGa(cid:1)bor Giczey 9TransformationandGeneManipulationinFilamentousFungi:AnOverview Robert L. Mach 10GeneticManipulationSystemsforNonconventionalFungi Johannes Wo€stemeyer, Anke Burmester, and Christine Schimek 11FungalMitochondria:Genomes,GeneticElements,andGeneExpression John C. Kennelland Stephanie M.Cohen © 2004 by Marcel Dekker, Inc. 12FungalEvolutionMeetsFungalGenomics Jessica Leigh, Elias Seif, Naiara Rodriguez-Ezpeleta,Yannick Jacob,and B. Franz Lang 13GenomeSequencePatternsandGeneRegulation:ABioinformaticsPerspective GautamB. Singh 14DNAChipsandMicroarrayAnalysis:AnOverview Sangdun Choi 15SignalTransductioninFungi:SignalingCascadesRegulatingVirulenceinFilamentousFungi Susanne Zeilinger II COMMERCIALAPPLICATIONS AND BIOTECHNOLOGICAL POTENTIAL 16ApplicationofGeneticEngineeringforStrainImprovementinFilamentousFungi Helena Nevalainen,ValentinoTe’o, andMerja Penttila€ 17TheGeneticImprovementofWineYeasts Isak S. Pretorius 18FungiinBrewing:BiodiversityandBiotechnologyPerspectives JørgenHansenand Jure Piskur 19Ethanol-ToleranceandProductionbyYeast Tah´ıa Ben´ıtez and Antonio C. Codo(cid:1)n 20Solid-StateFermentation:AnOverview Poonam Nigam, Tim Robinson, andDalel Singh 21BasicPrinciplesfortheProductionofFungalEnzymesbySolid-StateFermentation Gustavo Viniegra-Gonza(cid:1)lez and Ernesto Favela-Torres 22CommercialImportanceofSomeFungalEnzymes Rajendra K.Saxsena, BhawanaMalhotra,and AnoopBatra 23XylanasesofThermophilicMoldsandTheirApplicationPotential SeemaRawatand BhavdishN. Johri 24ChitinBiosynthesisinFungi Jose(cid:1) Ruiz-Herreraand Roberto Ruiz-Medrano 25BioactiveFungalPolysaccharidesandPolysaccharopeptides T. B. Ng 26BiotechnologicalPotentialofFungalLipids Michel Sancholle,Fre(cid:1)de(cid:1)ric Laruelle, Dorothy M.Lo€sel,and Je(cid:1)ro^me Muchembled 27IntroductiontotheTheoryofMetabolicModelingandOptimizationofBiochemicalSystems: ApplicationtoCitricAcidProductionin Aspergillusniger Ne(cid:1)stor V. Torres, Fernando Alvarez-Vasquez, and Eberhard O.Voit 28FungalCarotenoidProduction Javier Avalos and Enrique Cerda(cid:1)-Olmedo 29FungalTerpenoidAntibioticsandEnzymeInhibitors Shigeharu Inouye, Shigeru Abe, and Hideyo Yamaguchi © 2004 by Marcel Dekker, Inc. 30CommercialProductionandBiosynthesisofFungalAntibiotics:AnOverview S. Gutie(cid:1)rrez, R. E. Cardoza,J. Casqueiro, andJ. F. Mart´ın 31MolecularBiologyof Trichoderma andBiotechologicalApplications Merja Pentilla€, Carmen Limo(cid:1)n, and Helena Nevalainen 32Plectomycetes:BiotechnologicalImportanceandSystematics JuntaSugiyama and HiroyukiOgawa 33ExploitationofGFP-TechnologywithFilamentousFungi Dan FunckJensen andAlexander Schulz III MEDICAL BIOTECHNOLOGY 34AntifungalDrugsinFungalInfections Yoshimi Niwano 35AntitumorandImmunomodulatoryCompoundsfromFungi T. B. Ng 36ClinicalandLaboratoryDiagnosisofFungalInfections MalcolmRichardson and Simo Nikkari 37Candidiasis A. G.Palma-Carlos andM. Laura Palma-Carlos 38ImmunizationsAgainstFungalDiseasesinManandAnimals EstherSegal andDanielElad 39FungalAllergy Viswanath P. Kurup IV CULTURE COLLECTIONSAND BIOSAFETY 40CurrentStatusofFungalCollectionsandTheirRoleinBiotechnology DavidSmith andMatthew J. Ryan 41BenefitsandRisksofGeneticallyModifiedFoods:AnOverview FelicityGoodyear-Smith 42TransgenicMycoherbicides:NeedsandSafetyConsiderations JonathanGressel 43RecentDevelopmentsinBiotechnologyandIntellectualProperty, AccesstoGeneticResources,andBenefit-Sharing Phyllida Cheyne © 2004 by Marcel Dekker, Inc. Contributors ShigeruAbe InstituteofMedicalMycology,TeikyoUniversity,Tokyo,Japan FernandoAlvarez-Vasquez UniversidaddeLaLaguna,Tenerife,CanaryIslands, SpainandMedicalUniversityofSouthCarolina,Charleston,SouthCarolina,U.S.A. JavierAvalos UniversityofSeville,Seville,Spain AnoopBatra UniversityofDelhiSouthCampus,NewDelhi,India Tah´ıaBen´ıtez UniversidaddeSevilla,Sevilla,Spain DeepakBhatnagar AgriculturalResearchService,U.S.DepartmentofAgriculture, NewOrleans,Louisiana,USA AnkeBurmester Institutfu¨rMikrobiologie,Friedrich-Schiller-Universita¨tJena,Jena,Germany R.E.Cardoza UniversityofLeo´n,Ponferrada,andINBIOTEC,Leo´n,Spain JeffreyW.Cary AgriculturalResearchService,U.S.DepartmentofAgriculture, NewOrleans,Louisiana,USA J.Casqueiro UniversityofLeo´n,andINBIOTEC,Leo´n,Spain EnriqueCerda´-Olmedo UniversityofSeville,Seville,Spain Perng-KuangChang AgriculturalResearchService,U.S.DepartmentofAgriculture,NewOrleans,Louisiana, USA PhyllidaCheyne Barrister-at-law,Geneva,Switzerland SangdunChoi CaliforniaInstituteofTechnology,Pasadena,California,USA A.JohnClutterbuck InstituteofBiomedicalandLifeSciences,UniversityofGlasgow,Glasgow,Scotland,UK AntonioC.Codo´n UniversidaddeSevilla,Sevilla,Spain StephanieM.Cohen SaintLouisUniversity,St.Louis,Missouri,USA DanielElad KimronVeterinaryInstitute,BetDagan,Israel © 2004 by Marcel Dekker, Inc. AhmadM.Fakhoury NorthCarolinaStateUniversity,Raleigh,NorthCarolina,USA ErnestoFavela-Torres UniversidadAuto´nomaMetropolitana,Iztapalapa,D.F.,Me´xico Ga´borGiczey AgriculturalBiotechnologyCenter,Go¨do¨llo¨,Hungary FelicityGoodyear-Smith UniversityofAuckland,Auckland,NewZealand JonathanGressel WeizmannInstituteofScience,Rehovot,Israel S.Gutie´rrez UniversityofLeo´n,Ponferrada,andINBIOTEC,Leo´n,Spain JørgenHansen CarlsbergResearchLaboratory,Copenhagen-Valby,Denmark La´szlo´ Hornok AgriculturalBiotechnologyCenter,Go¨do¨llo¨,Hungary ShigeharuInouye InstituteofMedicalMycology,TeikyoUniversity,Tokyo,Japan MatthewJ.Ryan CABIBioscienceUKCentre,EghamSurrey,UnitedKingdom YannickJacob CanadianInstituteforAdvancedResearch,Universite´deMontre´al,Montre´al,Que´bec,Canada DanFunckJensen TheRoyalVeterinaryandAgriculturalUniversity,Copenhagen,Denmark BhavdishN.Johri G.B.PantUniversityofAgriculture&Technology,Pantnagar,India ShubhaP.Kale XavierUniversityofLouisiana,NewOrleans,Louisiana,USA JohnC.Kennell SaintLouisUniversity,St.Louis,Missouri,USA ViswanathP.Kurup MedicalCollegeofWisconsinandVAMedicalCenter,Milwaukee,Wisconsin,USA B.FranzLang CanadianInstituteforAdvancedResearch,Universite´ deMontre´al,Montre´al,Que´bec,Canada Fre´de´ricLaruelle Universite´ duLittoralCoˆted’Opale,CalaisCEDEX,France JessicaLeigh CanadianInstituteforAdvancedResearch,Universite´ deMontre´al,Montre´al,Que´bec,Canada CarmenLimo´n VTTBiotechnology,Finland DorothyM.Lo¨sel UniversityofSheffield,Sheffield,UnitedKingdom BenjaminC.K.Lu UniversityofGuelph,Guelph,Ontario,Canada RobertL.Mach InstituteforChemicalEngineering,ViennaTechnicalUniversity,Vienna,Austria BhawanaMalhotra UniversityofDelhiSouthCampus,NewDelhi,India J.F.Mart´ın UniversityofLeo´n,andINBIOTEC,Leo´n,Spain Je´roˆmeMuchembled InstitutCharlesQuentin,Pierrefonds,France HelenaNevalainen MacquarieUniversity,Sydney,Australia T.B.Ng TheChineseUniversityofHongKong,Shatin,NewTerritories,HongKong,China © 2004 by Marcel Dekker, Inc.
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