Handbook of Fungal Biotechnology, 2nd Edition, Revised and Expanded (Mycology, 20)

606 Pages·2003·4.73 MB·English

by  Dilip K. Arora

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
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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
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 use assystems 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
iii
iv Preface
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 fungal biotechnology, andcontributed chapters.
IamalsoindebtedtoMs.Sandra Beberman,VicePresident,Marcel Dekker, Inc.,andMs.DanaBigelow,Production
Editor, for their skill, patience,encouragement,guidance, and support.
DilipK. Arora
Contents
Preface iii
Contributors ix
I CELL BIOLOGY, BIOCHEMICAL AND MOLECULAR TECHNOLOGIES
1 Cell Biology ofHyphae 1
Oded Yarden
2 Protoplast Isolation,Regeneration, and Fusion inFilamentous Fungi 9
ShubhaP. Kale andDeepakBhatnagar
3 Metabolic Pathway Regulation 25
Perng-Kuang Chang and RichardB. Todd
4 FungalNuclei and Chromosomes 39
Benjamin C. K.Lu
5 Genomics of Filamentous Fungi: AGeneral Review 55
AhmadM. Fakhouryand Gary A.Payne
6 Stabilityand Instability of Fungal Genomes 69
A. JohnClutterbuck
7 Secondary Metabolic Gene Clusters inFilamentous Fungi 81
Jeffrey W.Cary
8 Application of Gene Cloning inFungalBiotechnology 95
La(cid:1)szlo(cid:1) Hornok andGa(cid:1)bor Giczey
9 Transformation and Gene Manipulationin Filamentous Fungi: AnOverview 109
Robert L. Mach
10 GeneticManipulation Systems for NonconventionalFungi 121
Johannes Wo€stemeyer, Anke Burmester, and Christine Schimek
11 FungalMitochondria:Genomes,Genetic Elements,and Gene Expression 131
John C. Kennelland Stephanie M.Cohen
v
vi Contents
12 FungalEvolutionMeets FungalGenomics 145
Jessica Leigh, Elias Seif, Naiara Rodriguez-Ezpeleta,Yannick Jacob,and B. Franz Lang
13 Genome Sequence Patterns and Gene Regulation: A Bioinformatics Perspective 163
GautamB. Singh
14 DNA Chipsand Microarray Analysis:An Overview 173
Sangdun Choi
15 Signal Transduction inFungi: Signaling Cascades Regulating Virulence in Filamentous Fungi 181
Susanne Zeilinger
II COMMERCIAL APPLICATIONS AND BIOTECHNOLOGICAL POTENTIAL
16 Application ofGenetic Engineering for Strain Improvement in Filamentous Fungi 193
Helena Nevalainen,ValentinoTe’o, andMerja Penttila€
17 The GeneticImprovement of Wine Yeasts 209
Isak S. Pretorius
18 Fungi inBrewing: Biodiversity and Biotechnology Perspectives 233
JørgenHansen and Jure Piskur
19 Ethanol-Tolerance and Production by Yeast 249
Tah´ıa Ben´ıtez and Antonio C. Codo(cid:1)n
20 Solid-State Fermentation: AnOverview 267
Poonam Nigam, Tim Robinson, andDalel Singh
21 Basic Principles for the Production ofFungalEnzymes by Solid-State Fermentation 275
Gustavo Viniegra-Gonza(cid:1)lez and Ernesto Favela-Torres
22 Commercial Importance of Some FungalEnzymes 287
Rajendra K.Saxsena, BhawanaMalhotra,and AnoopBatra
23 Xylanases ofThermophilic Molds and Their Application Potential 299
SeemaRawatand BhavdishN. Johri
24 Chitin Biosynthesis inFungi 315
Jose(cid:1) Ruiz-Herrera and Roberto Ruiz-Medrano
25 BioactiveFungalPolysaccharides and Polysaccharopeptides 331
T. B. Ng
26 Biotechnological Potentialof Fungal Lipids 341
Michel Sancholle,Fre(cid:1)de(cid:1)ric Laruelle, Dorothy M.Lo€sel,and Je(cid:1)ro^me Muchembled
27 Introduction tothe Theory ofMetabolic Modeling and Optimization of Biochemical Systems:
Application toCitric Acid Productionin Aspergillus niger 353
Ne(cid:1)stor V. Torres, Fernando Alvarez-Vasquez, and Eberhard O.Voit
28 FungalCarotenoidProduction 367
Javier Avalos and Enrique Cerda(cid:1)-Olmedo
29 FungalTerpenoid Antibioticsand Enzyme Inhibitors 379
Shigeharu Inouye, Shigeru Abe, and Hideyo Yamaguchi
Contents vii
30 Commercial Productionand Biosynthesis ofFungalAntibiotics: An Overview 401
S. Gutie(cid:1)rrez, R. E. Cardoza,J. Casqueiro, andJ. F. Mart´ın
31 Molecular Biology ofTrichoderma and BiotechologicalApplications 413
Merja Pentilla€, Carmen Limo(cid:1)n, and Helena Nevalainen
32 Plectomycetes: Biotechnological Importance and Systematics 429
JuntaSugiyama and HiroyukiOgawa
33 Exploitation ofGFP-Technology with Filamentous Fungi 441
Dan FunckJensen andAlexander Schulz
III MEDICAL BIOTECHNOLOGY
34 Antifungal Drugs inFungalInfections 453
Yoshimi Niwano
35 Antitumor andImmunomodulatory Compounds from Fungi 469
T. B. Ng
36 Clinical and Laboratory Diagnosis ofFungalInfections 479
Malcolm Richardson and Simo Nikkari
37 Candidiasis 493
A. G.Palma-Carlos andM. Laura Palma-Carlos
38 ImmunizationsAgainstFungalDiseases inMan and Animals 503
EstherSegal andDanielElad
39 FungalAllergy 515
Viswanath P. Kurup
IV CULTURE COLLECTIONSAND BIOSAFETY
40 Current Status of FungalCollectionsand Their Role inBiotechnology 527
DavidSmith andMatthew J. Ryan
41 Benefits and Risks ofGenetically Modified Foods:AnOverview 539
FelicityGoodyear-Smith
42 Transgenic Mycoherbicides: Needs and SafetyConsiderations 549
JonathanGressel
43 Recent Developments inBiotechnology and IntellectualProperty,
Access toGeneticResources, and Benefit-Sharing 565
Phyllida Cheyne
Index 575