Biotechnology and Biology of Trichoderma
- 1st Edition - April 7, 2014
- Editors: Vijai G. Gupta, Monika Schmoll, Alfredo Herrera-Estrella, Dr. R. S. Upadhyay, Irina Druzhinina, Maria Tuohy
- Language: English
- Hardback ISBN:9 7 8 - 0 - 4 4 4 - 5 9 5 7 6 - 8
- eBook ISBN:9 7 8 - 0 - 4 4 4 - 5 9 5 9 4 - 2
Biotechnology and Biology of Trichoderma serves as a comprehensive reference on the chemistry and biochemistry of one of the most important microbial agents, Trichoderma, and it… Read more
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Biotechnology and Biology of Trichoderma serves as a comprehensive reference on the chemistry and biochemistry of one of the most important microbial agents, Trichoderma, and its use in an increased number of industrial bioprocesses for the synthesis of many biochemicals such as pharmaceuticals and biofuels. This book provides individuals working in the field of Trichoderma, especially biochemical engineers, biochemists and biotechnologists, important information on how these valuable fungi can contribute to the production of a wide range of products of commercial and ecological interest.
- Provides a detailed and comprehensive coverage of the chemistry, biochemistry and biotechnology of Trichoderma, fungi present in soil and plants
- Includes most important current and potential applications of Trichoderma in bioengineering, bioprocess technology including bioenergy & biofuels, biopharmaceuticals, secondary metabolites and protein engineering
- Includes the most recent research advancements made on Trichoderma applications in plant biotechnology and ecology and environment
Microbiologists; biotechnologists; professionals, researchers, undergraduates, or post-graduates in bio-chemical engineering and biochemistry/biology; evolution and genetics researchers
Preface
Foreword
List of Contributors
Seation A Biology and Biodiversity
Chapter 1. Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats
Introduction
Methodology of Studying Trichoderma Biodiversity
Trichoderma Diversity in Different Habitats
Conclusions
Chapter 2. Ecophysiology of Trichoderma in Genomic Perspective
Trichoderma in Its Ecological Niche
From Diversity to Genomics
Mycotrophy of Trichoderma
Saprotrophy of Trichoderma on Dead Wood
Trichoderma Growth in Soil
Rhizosphere Competence of Trichoderma
Trichoderma versus Mycorrhizae
Trichoderma+Bacteria=?
Facultative Endophytism of Trichoderma
Animal Nourishment of Trichoderma
Most of the Famous Trichoderma Species are Environmental Opportunists
Versatile Carbon Utilization Patterns Reflect Ecological Specialization of Trichoderma spp.
Chapter 3. DNA Barcode for Species Identification in Trichoderma
Introduction
The Tools
Application of DNA Barcoding in Species-Level Identification of Trichoderma
Taxonomic Studies
Biodiversity Studies
Identification of Industrial Trichoderma Strains
Identification of Biocontrol Trichoderma Strains
Identification of Trichoderma Isolates with Clinical Relevance
Identification of Mushroom Pathogenic Trichoderma Strains
Conclusions
Chapter 4. Understanding the Diversity and Versatility of Trichoderma by Next-Generation Sequencing
Introduction
Access to Fungal and Trichoderma Diversity—Taxonomic Profiling
Plants Life under Control of Trichoderma—Functional Profiling
Conclusion
Chapter 5. Molecular Evolution of Trichoderma Chitinases
Introduction
Phylogeny and Evolution of the GH Family 18 Gene Family in Trichoderma
Subgroup A Chitinases
Subgroup B Chitinases
Subgroup C Chitinases
Conclusions
Section B Secretion and Protein Production
Chapter 6. Protein Production—Quality Control and Secretion Stress Responses in Trichoderma reesei
Introduction—Milestones of Trichoderma reesei
Protein Secretome of T. reesei
ER Quality Control and Secretion Stress Responses
Conclusion
Chapter 7. Heterologous Expression of Proteins in Trichoderma
Introduction
Promoter Options
Fusion Partners
Extracellular Proteases
Secretion Stress in the Frame
Mass Production of Heterologous Protein by Fermentation
N-glycosylation of Heterologous Proteins Produced in T. reesei
Conclusions
Chapter 8. Trichoderma Secretome: An Overview
Introduction
Proteomic Analysis of Secretory Proteins
Extraction of Extracellular Proteins for Proteomic Analysis
Extracellular Protein Secretion by T. reesei
Polysaccharide Degradation Machinery of T. reesei
New Candidates in Cellulose Degradation
Hemicellulose Hydrolyzing Enzymes
Lignin Degradation by T. reesei
Industrial Applications of T. reesei Cellulolytic Enzymes
Conclusion
Chapter 9. The Secretory Pathway in the Filamentous Fungus Trichoderma
Introduction
Translocation
Cotranslational Translocation
Post Translational Translocation
Protein Modifications in the ER
Vesicle Transport from ER to Golgi Complex and Trafficking within the Golgi Cisternae
Transport after Trafficking within the Golgi Complex
Secreted Proteins in Trichoderma
Concluding Remarks
Section C Secondary Metabolism
Chapter 10. Secondary Metabolism and Antimicrobial Metabolites of Trichoderma
Introduction
Peptaibols
Diketopiperazine-Like Compounds
Polyketides
Pyrones
Terpenes
Concluding Remarks and Future Directions
Chapter 11. Recent Advancements on the Role and Analysis of Volatile Compounds (VOCs) from Trichoderma
Introduction
Detection Techniques of VOCs
Types of Volatiles Compounds
Application of VOCs in Agriculture
Conclusion
Section D Tools
Chapter 12. Molecular Tools for Strain Improvement of Trichoderma spp.
Introduction
Genetic Transformation Techniques
Auxotrophic and Dominant Selection Markers
Marker Recycling Strategies and Marker Free Strains
Advanced Methods for Gene Targeting
RNA Mediated Gene Silencing
Promoters for Recombinant Protein Expression and Targeting
Concluding Remarks
Chapter 13. Genetic Transformation and Engineering of Trichoderma reesei for Enhanced Enzyme Production
Introduction
Engineering Cellulase and Hemicellulase Regulation
Homologous and Heterologous Gene Expression and Gene Disruption
Protein Engineering
Engineering Promoters
Conclusion
Chapter 14. Applications of RNA Interference for Enhanced Cellulase Production in Trichoderma
Introduction
RNA Interference in Fungus
Transcriptional Regulation of Cellulase Gene Expression
Application of Gene Downregulation Strategy for Enhanced Cellulase Production
Combination of RNAi and Overexpression of the Regulating Genes
Conclusions and Prospects
Chapter 15. RNAi-Mediated Gene Silencing in Trichoderma: Principles and Applications
Introduction
Molecular Mechanisms
Advantages and Disadvantages of Using RNAi-Mediated Gene Silencing as a Genetic Manipulation Tool in Filamentous Fungi
Strategies of Applying RNAi for Gene Silencing in Trichoderma and Other Filamentous Fungi
Conclusions
Section E Cellulases
Chapter 16. Cellulase Systems in Trichoderma: An Overview
Introduction
Degradation of Cellulose by Cellulase Systems
History of the Trichoderma Cellulase Research
Structural and Functional Diversity of Trichoderma Cellulases
Cellulase Systems and Complexes
Chapter 17. Use of Cellulases from Trichoderma reesei in the Twenty-First Century—Part I: Current Industrial Uses and Future Applications in the Production of Second Ethanol Generation
Overview of the Global Enzyme Market
Industrial Cellulases
Current Applications
Perspectives
Application of Trichoderma Cellulases in the Bioethanol Industry
Chapter 18. Use of Cellulases from Trichoderma reesei in the Twenty-First Century—Part II: Optimization of Cellulolytic Cocktails for Saccharification of Lignocellulosic Feedstocks
Genetics of Industrial Trichoderma reesei Strains
The T. reesei Enzyme Cocktail
Hydrolysis of Cellulose
Limitations in Lignocellulose Hydrolysis
Improvement of Enzyme Cocktails by Optimization of Enzyme Ratios
Improvement by Supplementation of T. reesei Enzyme Cocktails
Adapting Cellulose Cocktails to Process Conditions
Conclusions and Perspectives
Chapter 19. Beta-Glucosidase from Trichoderma to Improve the Activity of Cellulase Cocktails
Introduction
Cellulase Classification
Trichoderma reesei Cellulases
Trichoderma reesei BGLs
BGLs from Aspergillus oryzae
Synergism between Cellulases
Heterologous Expression of Cellulases
Yarrowia lipolytica Expression Platforms
Pichia pastoris Expression Platforms
β-Glucosidase from Trichoderma to Improve the Activity of Cellulase Cocktails
Chapter 20. Regulation of Glycoside Hydrolase Expression in Trichoderma
Introduction
Regulation by Environmental Parameters
Regulatory Mechanisms
Physiological Responses
Chapter 21. Trichoderma Proteins with Disruption Activity on Cellulosic Substrates
Structure and Occurrence of Cellulose in Nature
General Aspects of Cellulose Degradation
Cellulose Degradation by T. reesei
Cellulolytic Enzymes in Other Trichoderma Species
Chapter 22. Molecular Mechanism of Cellulase Production Systems in Trichoderma
Introduction
Cellulase System of T. reesei
Induction Mechanism of Cellulase Production
Promoter Involved in Cellulase Production
Molecular Mechanism of Cellulase Production
Approaches for Refining the Cellulases Production System in T. reesei
Chapter 23. Trichoderma in Bioenergy Research: An Overview
Introduction
Fungal Enzyme Systems and Trichoderma Technology
Industrial Applications of Trichoderma
Trichoderma Enzyme Systems in Bioenergy Research
Conclusion
Section F Industrial Applications
Chapter 24. Trichoderma Enzymes for Food Industries
Introduction
Fungus of Industrial Interest
Trichoderma Enzymes for Industries
Xylanases
Cellulases
Other Enzymes
Food Industry
Perspectives for Biotechnological Production of Enzymes by Trichoderma
Chapter 25. Trichoderma: A Dual Function Fungi and Their Use in the Wine and Beer Industries
Introduction
Application in the Wine and Beer Industries
Chapter 26. Trichoderma Enzymes for Textile Industries
Substrate
Enzymes
Textile Processes
Trichoderma Enzymes in Textile Finishing Processes
Trichoderma as a Production Host for Textile Enzymes
Future Trends
Chapter 27. Metabolic Diversity of Trichoderma
Introduction
Global Metabolism
Carbohydrate Metabolism and Glycoside Hydrolases
Energy Metabolism
Secondary Metabolism
Metabolism and Transporters
Chapter 28. Sequence Analysis of Industrially Important Genes from Trichoderma
Introduction
Gene Sequence Analysis Fundamentals
Genome Analysis of Trichoderma
Industrially Genes from Trichoderma
Sequence Analysis of Industrially Genes from Trichoderma
Conclusion
Chapter 29. Biosynthesis of Silver Nano-Particles by Trichoderma and Its Medical Applications
Introduction
SNP Biosynthesis
Mechanism
Medical Application
Chapter 30. Role of Trichoderma Species in Bioremediation Process: Biosorption Studies on Hexavalent Chromium
Introduction
Hexavalent Chromium Bioremediation will be Discussed Here with a Case Study Representing Chromium Biosorption by Trichoderma Species
Conclusion
Section G Biocontrol and Plant Growth Promotion
Chapter 31. Applications of Trichoderma in Plant Growth Promotion
Introduction
Trichoderma as a Plant Growth Promoter
Consistency of Growth Promotion
Commercialization
Mechanisms of Growth Promotion
Conclusions
Chapter 32. Molecular Mechanisms of Biocontrol in Trichoderma spp. and Their Applications in Agriculture
Introduction
Mycoparasitism
Morphological Changes
Roll of Cell Wall Degrading Enzymes
Signal Transduction in Mycoparasitism
ROS-Nox-Signal Transduction
Antibiosis (Secondary Metabolites Involved in Biocontrol)
Pyrones
Polyketides
Nonribosomal Peptides
Mycotoxins Produced by Trichoderma spp.
Synergism between Enzymes and Antibiotics
Competition for Nutrients
Plant Growth Promotion by Trichoderma
Plant Root Colonization
Induction of Systemic Resistance to Plants by Trichoderma spp.
Signal Transduction Pathways that Mediate Trichoderma-Plant Communication
Trichoderma Elicitor of Systemic Resistance in Plants
Signal Transduction during Plant–Trichoderma Interaction in Trichoderma
Transgenic Plants Expressing Trichoderma Genes
Concluding Remarks
Chapter 33. Genome-Wide Approaches toward Understanding Mycotrophic Trichoderma Species
Introduction
Lessons from the Genome Sequence
Transcriptome Analyses
The Functional Genomics View of Mycoparasitism
High-Throughput Analysis of the Trichoderma-Plant Interaction
Future Directions
Concluding Remarks
Chapter 34. Insights into Signaling Pathways of Antagonistic Trichoderma Species
Introduction
G Protein Signaling
Effector Pathways of G Protein Signaling in Fungi
Signaling Pathways and Characterized Components in Trichoderma Species
Signal Transduction Components and Pathways Affecting Vegetative Growth and Conidiation
The Role of Signaling in Trichoderma Mycoparasitism and Biocontrol
Conclusions
Chapter 35. Enhanced Resistance of Plants to Disease Using Trichoderma spp.
Introduction
Induced Disease Resistance in Plants
Induced Resistance by Trichoderma spp.
Signaling Pathways of Trichoderma-Induced Resistance
Trichoderma spp.-Secreted Elicitors of Plant Resistance
Engineering Plants for Disease Resistance Using Trichoderma Genes
Combination of Trichoderma with Other Beneficial Microorganisms
Other Effects of Trichoderma spp. Inoculation to the Plant
Conclusion
Chapter 36. Enhanced Plant Immunity Using Trichoderma
Introduction
Mechanisms of Plant Protection by Microbes
Trichoderma-Induced Immunity
Plant Protection Conferred by Trichoderma
Conclusions
Chapter 37. Genes from Trichoderma as a Source for Improving Plant Resistance to Fungal Pathogen
Introduction
Trichoderma Inducing Resistance in Plants
Transgenic Plants Expressing Trichoderma Genes Develop Increased Resistance to Fungal Pathogens
Trichoderma Genes Involved in Elicitation of ISR
Conclusion
Abbreviations
Chapter 38. Trichoderma Species as Abiotic Stress Relievers in Plants
Introduction
Microbes for the Management of Abiotic Stresses
Alleviation of Abiotic Stress in Plants by Trichoderma
Alleviation of Drought Stress in Plants by Trichoderma
Alleviation of Salinity Stress in Plants by Trichoderma
Alleviation of Heat Stress in Plants by Trichoderma
Trichoderma Genes for Abiotic Stress Tolerance
Mechanism of Abiotic Stress Tolerance Using Trichoderma
Host Gene: Stress Tolerant Varieties
Conclusion
Chapter 39. Advances in Formulation of Trichoderma for Biocontrol
Introduction
Types of Formulation
Microencapsulation
Enhancement of Shelf Life and Application Efficiency
Compatibility with Other Biological Systems
Conclusion and Future Prospects
Chapter 40. Trichoderma: A Silent Worker of Plant Rhizosphere
Introduction
Diverseness Amongst Trichoderma
Trichoderma as Inducer of Plant Defense Response
Trichoderma as a Biofertilizer and Plant Growth Promoter
Commercialization
Trichoderma Genes Responsible for Playing “Big Games”
Conclusion
Index
- Edition: 1
- Published: April 7, 2014
- Language: English
VG
Vijai G. Gupta
Dr Vijai G. Gupta is an Assistant Professor of Biotechnology at MITS University of India. Currently he is working as Research Scientist at National University of Ireland in Galway. Dr. Gupta’s present work is focused on the development and optimization of novel Enzyme-based bioconversion systems for biorefining and bioenergy. He has been honored with several awards, including the prestigious Indian ICAR Senior Research Fellowship and Indian Young Scientist Award. He has submitted 33 new fungal nucleotide sequences and deposited 147 fungal strains in International databases. His work with Fusarium spp., Colletotrichum gloeosporioides, Penicillium spp. and Trichoderma spp. is augmented by contributions to biotechnological development, molecular diversity, secondary metabolites and industrial applications
Dr. Gupta is the editor-in-chief of the International Journal of Plant Pathology and a regional editorial board member of 8 other respected journals. He is the author of 40 journal articles and 27 book chapters. Gupta has also written and edited books and series from reputed publishers, including CRC Press, Taylor and Francis, USA; Springer, USA; Elsevier, USA; Nova Science Publisher, USA and LAP Lambert Academic Publishing, Germany.
Affiliations and expertise
Department of Chemistry and Biotechnology, Tallinn University of Technology, EstoniaMS
Monika Schmoll
Dr. Monika Schmoll received her degree (1999) and Ph. D. (2003) on regulation of cellulase expression and signal transduction in the filamentous fungus Hypocrea jecorina (Trichoderma reesei) at the Vienna University of Technology. Besides gaining postdoctoral experience and building her own group at the Vienna University of Technology, she has been a visiting scientist in the laboratory of Professor N. Louise Glass (Department of Plant and Microbial Biology, University of California, Berkeley, USA), the University of Rome La Sapienza and the University of Szeged, Hungary. She is author of 33 publications and 2 book chapters. Currently, Dr. Schmoll is group leader in the Research Area Molecular Biotechnology at the Vienna University of Technology. The primary research field of Dr. Schmoll is the interconnection between light response, sexual development and cellulase gene expression in Trichoderma reesei. She showed for the first time that cellulase gene expression is modulated by light in T. reesei and could since then elucidate important mechanistic details on the underlying mechanism. Her group discovered the sexual cycle in the biotechnological workhorse Trichoderma, which had previously considered asexual. This work was published in PNAS in 2009 and since then investigation of this phenomenon and its peculiarities in Trichoderma has become an additional focus. Her work with Trichoderma is complemented by contributions to genome annotation of several fungi (Trichoderma spp., Aspergillus nidulans, Postia placenta, Ceriporiopsis subvermispora), especially in the field of signal transduction.
Affiliations and expertise
Vienna University of Technology, AustriaAH
Alfredo Herrera-Estrella
Prof. Alfredo Herrera-Estrella grew up in Mexico City and graduated from the National School of Biological Sciences in 1985. He did his graduate research (1986-1990) with Prof. Marc Van Montagu at the State University of Ghent, Belgium, studying the T-DNA transfer process from Agrobacterium tumefaciens to plants. He described for the first time Agrobacterium virulence proteins capable of carrying the T-DNA into the plant cell nucleus, and began to study the mycoparasitic process of the biocontrol agent Trichoderma atroviride. Dr. Herrera-Estrella pioneered the development of molecular tools for the study of a biocontrol agent with the establishment of transformation systems, and cloning of the first mycoparasitism related genes. Such developments opened possibilities for strain improvement. He continued those studies while at the Genetic Engineering Department of the Irapuato Unit of Cinvestav (1991-2004), and began studies towards the elucidation of the mechanisms involved in light perception in Trichoderma. In 2000, he was awarded the prize of the Mexican Academy of Sciences. By 2004, he got involved in the establishment of the National Laboratory of Genomics for Biodiversity. Since then he and his group have been involved in Functional Genomics Projects, including the elucidation of the complete maize genome, and the development of advanced techniques to study gene expression by deep sequencing. Dr. Herrera-Estrella has continuing efforts in the elucidation of signaling cascades triggering asexual development in fungi. In particular his group has been using functional genomics approaches for this purpose, and recently has been involved in the study of the role of reactive oxygen species as signal molecules in injury responses in fungi.
Affiliations and expertise
National Laboratory of Genomics for Biodiversity, MexicoDU
Dr. R. S. Upadhyay
Professor R. S. Upadhyay (b. November 15, 1955) received his M. Sc. (1976) and Ph. D. (1980) degrees from Banaras Hindu University (BHU), Varanasi, India. Since then he has been actively engaged in research. His main focus on research has been on biological control of plant pathogens, programmed plant cell death in response to pathogens, bioremediation of toxic effluents, induced resistance in plants and their immunization, plant growth promoting microbes, chitinase production from actinomycetes, mycorrhizal technology for reclamation of wastelands, role rhizobacteria in detoxifying phytotoxic effects, development of molecular markers in tracking microbes in environment, effect of biotic and abiotic factors on plants, and molecular basis of plant-microbe interaction specially for Trichoderma spp. & Fusarium spp. His work has been well cited internationally. He has been working at Banaras Hindu University in various positions such as Lecturer, (1984-88), Senior Lecturer, (1988-1991), UGC Research Scientist-B, BHU (1988-1991 on lien from BHU), Reader, Banaras Hindu University (1991-1999, appointed in absentia), Professor, (1999 till date), Student Advisor, Faculty of Science, BHU (2010-11), Coordinator, Environmental Science, BHU (2011 till date) and Dy. Coordinator, Centre of Advanced Study in Botany, BHU (2011, for five years). He has been recipient of six prestigious national fellowships of the Government of India. He is recipient of five national awards in the area of science, two conferred by the Prime Minister of India. In addition he worked in prestigious foreign laboratories as visiting Scientist of The Royal Society, London (1988-89), Research Associate of NIH, U.S.A. (1990-91), and INSA- JSPS Fellowship, Japan (1994-95). He has also visited many other courtiers to participate in International conferences or for delivering invited lectures.
Affiliations and expertise
Banaras Hindu University, IndiaID
Irina Druzhinina
Dr. Irina Druzhinina studied biology at the Lomonosov’s State University in Moscow, Russia, and at the University of Vienna, where she graduated (PhD) in 2001. Thereafter she became a University Assistant in the research area of C.P. Kubicek at Vienna University of Technology, and habilitated in 2011 in “Microbiology”. She is now leader of the working group “Microbiology” at the same institute.
The scientific work of Irina Druzhinina started with a focus on mycology and molecular evolution, working on species diversity and population differentiation in Trichoderma, where she established an online tool for species identification based on DNA barcodes that is today one of the main resources for this purpose for researchers worldwide. In addition, she worked on such diverse topics as phenotype profiling of industrial fungi, peptaibol biosynthesis in Trichoderma, biodiesel production by marine algae, Trichoderma endophytes, biofungicide development and molecular ecology of Trichoderma. In the last years, her interest expanded to ecological genomics, i.e. the use of genome wide information to study the evolutionary adaptation of Trichoderma in its habitats. She acts as a member of the editorial board for Applied and Environmental Microbiology, and is the chair of the International Subcommission on Taxonomy of Trichoderma and Hypocrea, a member of ICTF/IUMS. She published > 60 papers in peer reviewed international journals and edited a book
Affiliations and expertise
Plants Nutrition Department, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityMT
Maria Tuohy
Dr. Maria G. Tuohy is the Head of the Molecular Glycobiotechnology Research Group, Department of Biochemistry, School of Natural Sciences, NUI Galway which has developed a strong track record in Glycobiotechnology and Enzyme Biotechnology. She has more than 20 years experience in the molecular biochemistry, genetics and biotechnology of fungi, with a special interest in thermophilic ascomycetes and the characterization of these fungi as cell factories for protein production, including novel thermostable enzymes/enzyme systems. Dr. Tuohy and her group have developed patented enzyme-based technologies for key bioenergy and biorefinery applications from terrestrial and marine biomass and wastes, including 3rd generation feedstocks. The group also investigates the use of enzymes for the recovery and selective modification of high-value biochemicals and plant carbohydrate-derived bioactives (‘Glycobioengineering’). Dr. Tuohy is a PI in the Energy Research Centre, NUI, Galway and the recently funded national Bioenergy and Biorefinery Competence Centre, is a member of the EU FP7 Biofuels Platform and a national research PhytoNetwork. Dr. Tuohy has been a visiting researcher in RUGhent, Belgium and BSH Institut fur Holzchemie, Hamburg. Dr. Tuohy is author of ~132 research publications, including refereed publications, book chapters, conference papers poster/short communications. She is also a reviewer for international journals and funding agencies and several books as co-editor- Springer Science Publisher, USA; CRC Press, Taylor and Francis, USA; Germany; Nova Science Publisher, USA and Elsevier Press, USA (under Progress) with Dr. V. K. Gupta
Affiliations and expertise
Head of the Molecular Glycobiotechnology Research Group, Department of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, IrelandRead Biotechnology and Biology of Trichoderma on ScienceDirect