Handbook of Fungal Biotechnology Second Edition, Revised and Expanded

569 Pages·2004·6.89 MB·English

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.
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© 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.