Progress in Mycology: Biology and Biotechnological Applications

Preface
Contents
Editors and Contributors
About the Editors
Contributors
Part I: Fungal Enzymes
1: Progress in Fungal Mannanolytic Enzyme Research in India
1.1 Introduction
1.2 β-Mannanases
1.3 Accessory Mannanolytic Enzymes
1.4 Guar Gum: Indian Scenario
1.5 Conclusions and Future Perspectives
References
2: Thermophilic Fungal Lignocellulolytic Enzymes in Biorefineries
2.1 Introduction
2.2 Pretreatment Technologies
2.3 Enzymes Involved in Lignocellulosic Degradation
2.3.1 Cellulases
2.3.2 Hemicellulases
2.4 Lytic Polysaccharide Monooxygenases (LPMOs)
2.5 Secretome-Based Analysis of Lignocellulolytic Enzymes
2.6 Commercially Important Producers of Lignocellulolytic Enzymes
2.7 Designing Lignocellulolytic Enzyme Cocktails for 2G Ethanol Production
2.8 Approaches for Developing Cellulolytic Enzyme Cocktails
2.9 Statistical Optimization of Cellulolytic Cocktails
2.10 Conclusions and Future Perspectives
References
3: Fungal Glucoamylases: Developments in India and Recent Trends
3.1 Introduction
3.2 Fungal Glucoamylase Research in India
3.3 Glucoamylase Production
3.4 Mutation, Cloning, and Production of Recombinant Glucoamylase
3.5 Purification and Characterization
3.6 Structure of Fungal Glucoamylase
3.6.1 Catalytic Domain
3.6.2 Starch-Binding Domain (SBD)
3.7 Applications of Glucoamylase
3.7.1 Production of Dextrose Syrup
3.7.2 Alcoholic Fermentation
3.7.3 Fabric Industry
3.7.4 Raw Starch Digestibility
3.8 Conclusions
References
4: Developments in Fungal Phytase Research: Characteristics and Multifarious Applications
4.1 Introduction
4.2 Developments in Fungal Phytase Research in India
4.3 Brief Description of Methods of Phytase Production
4.3.1 Phytase Production by Microbes
4.3.2 Production of Phytases by Recombinant Microbes
4.4 Purification and Characteristics of Phytase
4.5 Multifarious Applications of Fungal Phytases
4.5.1 Ameliorating the Nutritional Status of Foods and Feeds
4.5.1.1 Applications in Animal Nutrition
4.5.1.2 Applications in Aquaculture/Fish Farming
4.5.1.3 Applications in Human Nutrition
4.5.2 Mitigation of Environmental Phosphorus Pollution
4.5.3 Plant Growth Promotion and Soil Amendment
4.5.4 Generating Specific Myo-inositol Phosphates for Use in Therapeutics
4.5.5 Virtual Peroxidises Derived from Phytases
4.5.6 Other Applications of Fungal Phytases
4.6 Future Perspectives
4.7 Conclusions
References
5: Fungi in Biofuel Research
5.1 Introduction
5.2 Types of Biofuels
5.3 National Policy
5.4 Fungal Potential
5.5 Fungal Secretory Enzymes
5.5.1 Cellulases
5.5.1.1 Cellobiohydrolase (CBHI)
5.5.1.2 Endoglucanase
5.5.1.3 β-Glucosidases
5.5.2 Hemicellulases
5.5.3 Ligninolytic Enzymes
5.5.4 Auxiliary Activity Enzymes
5.5.5 Pectinases
5.5.6 Amylases
5.5.7 Lipases
5.5.8 Carbohydrate-Binding Modules
5.6 Classification in the CAZy Database
5.7 The Role of Fungi in Bioethanol Production
5.7.1 First-Generation Bioethanol
5.7.2 Second-Generation Bioethanol
5.7.2.1 Pretreatment
5.7.2.2 Enzymatic Saccharification
5.8 Fungi in Biodiesel Production
5.9 Regulation of Enzyme Production in Fungus
5.10 Strain Improvement
5.11 Research and Development in Academia and Industries
5.12 Conclusions and Future Perspectives
References
6: Ligninolytic Fungi from the Indian Subcontinent and Their Contribution to Enzyme Biotechnology
6.1 Introduction
6.2 Lignin-Degrading Fungi
6.3 Lignin-Degrading Enzymes
6.3.1 Laccases: The Leading Industrial Biocatalyst
6.3.2 Lignin Peroxidases: General Properties and Mechanism
6.3.3 Manganese Peroxidases: Characteristics and Functions
6.3.4 Versatile Peroxidase: A Superior Lignin Degrader
6.3.5 Dye-Decolorizing Peroxidases
6.3.6 Accessory Enzymes for Lignin Degradation
6.4 Biotechnological and Industrial Applications of Ligninolytic Fungi and Enzymes
6.4.1 Biofuel Industry: Delignification and Detoxification
6.4.2 Food, Feed, and Beverage Industry
6.4.3 Paper and Pulp Industry: Biopulping, Biobleaching, and Deinking
6.4.4 Transformation and Degradation of Textile Dye Effluents
6.4.5 Bioremediation of Hazardous Pollutants
6.5 Concluding Remarks
References
7: Fungal Chitinolytic Enzymes
7.1 Introduction
7.2 Chitin Metabolism in Fungi
7.2.1 Biosynthesis of Chitin and Chitosan
7.2.2 Structure-Function Relationship of Fungal Chitinolytic Enzymes
7.2.3 Classification of Chitinolytic Enzymes
7.3 Biochemical Characteristics of Chitinolytic Enzymes
7.3.1 Chitinases
7.3.2 Chitosanases
7.3.3 Chitin Deacetylases
7.4 Molecular Studies of Chitinolytic Enzymes
7.5 Roles of Chitinolytic Enzymes in Fungal Growth and Differentiation
7.6 Application-Oriented Biological Roles of Fungal Chitinolytic Enzymes
7.6.1 Fungus-Fungus and Fungus-Insect Interactions
7.6.2 Chitinolytic Enzymes in Biocontrol of Plant Pathogenic Fungi and Insects
7.6.3 Chitinases in Single-Cell Protein Production
7.6.4 Production of Chitooligosaccharides
7.7 Epilogue
References
Part II: Production and Applications of Fungal Nanoparticles
8: Insight into Fungi-Mediated Nano-synthesis for Healthcare Applications: An Indian Perspective
8.1 Introduction
8.2 Classification of Nanoparticles
8.3 Types of Nanoparticles
8.3.1 Organic Nanoparticles
8.3.2 Inorganic Nanoparticles
8.3.3 Carbon-Based Nanoparticles
8.4 Synthesis and Characterization of Nanoparticles
8.5 Green Synthesis of Nanoparticles
8.5.1 Plant-Mediated Synthesis of Nanoparticles
8.5.2 Bacteria-Mediated Synthesis of Nanoparticles
8.5.3 Virus-Mediated Synthesis of Nanoparticles
8.5.4 Fungi-Mediated Synthesis of Nanoparticles
8.5.4.1 Methods for Fungi-Mediated Synthesis of Nanoparticles
8.5.4.2 Factors Involved in Mycosynthesis of Nanoparticles
8.5.4.3 Mechanism of Fungi-Mediated Nano-Synthesis
8.6 Applications of Nanoparticles Synthesized Using Fungi in Healthcare
8.6.1 Antimicrobial Activity
8.6.2 Antioxidant Activity
8.6.3 Anticancer/Cytotoxic Activity
8.6.4 Larvicidal Activity
8.6.5 Wound-Healing Activity
8.6.6 Drug Delivery
8.6.7 Sensing
8.7 Conclusions and Future Prospects
References
9: Mycofabrication of Metal Nanoparticles: A Green Approach
9.1 Introduction
9.2 Mycofabrication of Metal Nanoparticles
9.3 Why Mycofabrication?
9.4 Mycofabrication, a Green Approach
9.5 Mechanistic Aspect
9.6 Conclusions and Perspectives
References
10: Nanosensors for the Detection of Plant and Human Fungal Pathogens
10.1 Introduction
10.2 Plant Pathogens and Current Ways of Their Detection
10.3 Human Pathogens and Current Ways of Their Detection
10.4 Nanomolecular Methods for Detection of Plant and Human Pathogenic Fungi
10.4.1 Nanoparticles for Improved Molecular Diagnostics
10.4.2 Lateral Flow Assays
10.4.2.1 Detection of Plant Pathogens
10.4.2.2 Detection of Human Pathogens
10.4.3 Rapid Nano-LAMP Assay
10.4.4 Array Biosensors
10.4.5 Lab on a Chip
10.5 Portable Genome Sequencer (Nanopore Sequencing System)
10.5.1 Magnetic Nanoparticles for Barcodes and NMR
10.6 Conclusions
References
Part III: Plant/Human Fungal Pathogens and Their Control
11: Milestones in Medical Mycology in India
11.1 Introduction
11.1.1 A Brief Historical Account
11.1.2 Early Progress of Medical Mycology in India
11.1.3 Book, Manual, and Chapter in a Book
11.1.4 Discovery of New Species of Human Pathogenic Fungi, Novel Pathogens, and Lab Techniques
11.1.5 Recent Progress of Medical Mycology in Different Institutions in India
11.2 Training in Medical Mycology
11.2.1 Strengthening Laboratory Facilities in Medical Mycology
11.2.2 Community Studies in Fungal Infections and Preventive Measures
11.2.3 Herbal Therapy
11.2.4 ISMM (ISHAM) Awards
11.2.5 ISMM (ISHAM Newsletter)
References
12: Fungal Enzymes in Biocontrol of Phytopathogens
12.1 Introduction
12.2 Fungi as Biocontrol Agents
12.2.1 Trichoderma as Biocontrol Agent
12.3 Mycoparasitism
12.4 Major Fungal Enzymes in Biocontrol
12.4.1 Proteases
12.4.2 Glucanases
12.4.2.1 beta-Glucanases
12.4.2.2 Biocontrol Action of Glucanase
12.4.3 Chitinases
12.5 Regulation of Mycoparasitism
12.5.1 Host Recognition and Signaling Pathways
12.5.2 Transcription Factors in Biocontrol
12.6 Conclusion and Future Perspectives
References
13: Candida: A Model Fungus to Study Differentiation, Pathogenesis, and Bioprospecting
13.1 Introduction
13.2 Human Fungal Pathogens
13.3 Human Pathogenic Candida Species
13.3.1 C. albicans
13.3.2 C. glabrata
13.3.3 C. tropicalis
13.3.4 C. auris
13.3.5 C. parapsilosis
13.4 Evolutionary Relatedness in Candida Species
13.5 Morphological Switching and Virulence in Candida
13.6 Multidrug Resistance in Candida
13.7 Bioprospecting of Candida Species
13.7.1 Candida in Ethanol Production
13.7.2 Candida in Wine Fermentation
13.7.3 Candida in Sugar Alcohol Production
13.7.4 Candida in Long-Chain Dicarboxylic Acid Production
13.7.5 Oleaginous Yeast: Candida phangngensis
13.7.6 Use of Candida to Develop Recombinant Strains
13.8 Candida Research: An Indian Prospective
13.9 Epilogue
References
14: Research Contributions from India on Membrane-Modifying Peptides: Motivations from Fungal Peptaibiotics
14.1 Introduction
14.1.1 Molecular Properties
14.1.2 Analytical Techniques
14.1.3 Peptaibol/Peptaibiotic Research in India
14.2 Chemical Synthesis and Molecular Structural Characterization
14.2.1 Peptaibol Synthesis
14.2.2 Nuclear Magnetic Resonance (NMR) Studies
14.2.3 Crystal Structures
14.3 Mass Spectrometric Characterization
14.3.1 Applications of MS to Sequence Peptaibols
14.3.1.1 Use of Different Ionization Modes
14.3.1.2 Role of Mass Analysers and Tandem Mass Spectrometry
14.3.2 In vitro Chemical Conversion of Elvapeptins to Efrapeptins Probed by ESI-MS
14.3.3 ESI-Ion Trap MS/MS Studies on Peptaibols
14.3.3.1 ESI-CID MS/MS Reveals Microheterogeneous Trichotoxin Sequences
14.3.3.2 ESI-ETD MS/MS in Conjunction with CID for Distinguishing Leu from Ile in Peptaibol Sequences: Application of MS3 on Z...
14.3.4 ESI-Q-TOF MS/MS of Lipopeptaibols and Peptaibols from the Himalayan Cold Habitat Fungus
14.3.5 Intact Cell Mass Spectrometry (ICMS) by MALDI-TOF MS of Peptaibols
14.4 Biosynthesis
14.5 Biophysical and Biological Functions
14.5.1 Channel-Forming Ionophores and Uncouplers of Mitochondrial Oxidative Phosphorylation
14.5.2 Antimalarial Activity
14.5.3 Cytotoxic Activity
14.6 Future Perspectives
References
15: Development of Mycotoxicology in India
15.1 Introduction
15.2 Historical Records of Mycotoxicoses
15.3 Outbreaks of Mycotoxicoses in India
15.4 Mycotoxins, Types of Toxicity and Risk Assessment
15.5 Natural Occurrence of Mycotoxins in Indian Foods and Feeds
15.5.1 Mycotoxin Contamination in Cereal Grains
15.5.2 Mycotoxin Contamination in Animal Feeds
15.5.3 Mycotoxin Contamination in Dried Medicinal Plants
15.5.4 Mycotoxin Contamination in Fresh Fruits and Vegetables
15.5.5 Mycotoxin Contamination in Sun-Dried Fruits, Vegetables and Nuts
15.5.6 Mycotoxin Contamination in Spices and Condiments
15.5.7 Mycotoxin Contamination in Oil Seeds, Cakes and Oils
15.5.8 Mycotoxin Contamination in Other Consumables
15.6 Detection of Mycotoxins
15.7 Strategies for the Management of Mycotoxins
15.7.1 Preharvest Strategies
15.7.2 Post-harvest Strategies
15.8 Conclusions and Future Perspectives
References
16: Fungi a Potential Source of Bioactive Metabolites an Indian Prospective
16.1 Introduction
16.2 Preliminary Work
16.3 Bioactives from Soil Fungi
16.4 Compounds Produced by Endophytic Fungi
16.4.1 Taxol from Endophytic Fungi
16.4.2 Compounds Other Than Taxol from Endophytic Fungi
16.4.3 Metabolites with Anti-inflammatory Activity
16.4.4 Metabolites with Antidiabetic Activity
16.4.5 Metabolites with Antimicrobial Activity
16.5 Useful Strategies to be Adopted in Cultivation of Fungi
16.5.1 One Strain, Many Compounds (OSMAC)
16.5.2 Metabolite Expression Modulated by Epigenetic Modifiers
16.5.3 Co-culture of Different Strains
16.6 Conclusions and Future Perspectives
References
Part IV: Bioprospecting of Fungi
17: Fungal Pigment Research in India: An Overview
17.1 Introduction
17.2 Investigations on Fungal Pigments in India
17.3 Pigment-Producing Fungi from India
17.4 Optimization of Pigment Production
17.5 Technologies for Enhancing Pigment Production
17.5.1 Media Optimization
17.5.2 Optimization of Fermentation Parameters
17.5.3 Co-culturing
17.5.4 Strategies/Modes of Cultivation and Extraction
17.5.5 Technologies for Enhancing Pigment Production
17.5.6 Cost-Effective Downstream Processing and Metabolic Engineering
17.5.7 Metabolic Engineering Using the CRISPR-Cas9 System
17.6 Microencapsulation, Nano-emulsions, and Nano-formulations
17.7 Addressing Toxicity Issue
17.8 Conclusions and Future Perspectives
References
18: Bioprospecting of Marine Fungi
18.1 Introduction
18.2 Natural Products from Marine Fungi
18.3 Economically Important Compounds Isolated and Identified from India
18.4 Present Status of Fungal Metabolites
18.5 Potential Applications and Future Perspectives
18.6 Conclusions
References
19: Recent Developments and Future Prospects of Fungal Sophorolipids
19.1 Introduction
19.1.1 Sophorolipid-Producing Strains
19.1.2 Sophorolipid Structure
19.2 Biosynthesis of Sophorolipids
19.2.1 Carbon Source
19.2.2 Nitrogen Source
19.3 Types of Biosurfactant Produced by Yeast/Fungi
19.4 Advantages of Biosurfactants Over Normal Surfactants
19.5 Availability of Raw Materials
19.6 Diversity
19.7 Selectivity and Specificity
19.8 Low Toxicity
19.9 Biodegradability
19.10 Applications
19.10.1 Antibacterial Activity
19.10.2 Anticancer Activity
19.10.3 Antifungal activity
19.10.4 Drug Delivery System
19.10.5 Cosmetics
19.10.6 Bioremediation
19.10.7 Immunomodulatory Activity
19.11 Conclusions and Future Perspectives
References
20: Fungi: A Sustainable and Versatile Tool for Transformation, Detoxification, and Degradation of Environmental Pollutants
20.1 Introduction
20.2 Bioremediation
20.3 Mycoremediation
20.4 Fungal Enzymes in Bioremediation
20.5 Fungi-Assisted Bioremediation of Various Organic as Well as Inorganic Pollutants.
20.5.1 Bioremediation of Dyes
20.5.2 Bioremediation of Poly-Aromatic Hydrocarbons (PAHs)
20.5.3 Bioremediation of Heavy Metals
20.5.4 Bioremediation of Pesticides
20.5.5 Bioremediation of Miscellaneous Pollutants
20.6 Fungal Genomics and Proteomics in Bioremediation
20.7 Conclusions and Future Prospects
References
21: Heterologous Protein Expression in Yeast and Molds
21.1 Introduction
21.2 Different Expression Platforms
21.2.1 Introduction
21.2.2 Heterologous Protein Expression in Yeast
21.3 Components of a Yeast Expression System
21.3.1 Host Strains
21.3.2 Vectors and Promoters
21.3.2.1 Saccharomyces cerevisiae
21.3.2.2 Pichia pastoris
21.3.2.3 Yarrowia lipolytica
21.3.2.4 Promoters Used in Other Fungi and Yeast
21.3.3 Selection Marker
21.3.4 Secretion Signals
21.3.5 Recovery of Intracellular Proteins
21.3.6 Affinity Tags and Protein Purification
21.4 Yeast Expression Platforms
21.4.1 Saccharomyces cerevisiae as an Expression Host
21.4.2 Pichia pastoris as an Expression Host
21.4.3 Hansenula polymorpha as an Expression Host
21.4.4 Kluyveromyces sp. as an Expression Host
21.4.5 Yarrowia lipolytica as an Expression Host
21.4.6 Zygosaccharomyces sp. as an Expression Host
21.4.7 Candida boidinii as an Expression Host
21.4.8 Debaryomyces sp. as an Expression Host
21.4.9 Arxula adeninivorans as an Expression Host
21.4.10 Aspergillus sp. as an Expression Host
21.4.11 Other Fungi as Hosts for Recombinant Protein Production
21.5 Metabolic Engineering and Systems Biology for Strain Improvement
21.5.1 Introduction
21.5.2 Introduction of Genetic Variability in Yeast
21.5.2.1 Genome Shuffling
21.5.2.2 Cytoduction
21.5.2.3 Directed Evolution
21.5.2.4 Metabolic Engineering
21.5.2.5 Inverse Metabolic Engineering
21.5.2.6 Synthetic Biology
21.6 Yeast Cell Surface Display Technology
21.6.1 Introduction
21.6.2 Applications of Yeast Cell Surface Display
21.7 Yeast Expression Systems: Contribution by Indian Scientists and Authors
21.8 Recombinant Gene Expression and Bioprocess Optimization Using Yeast Expression System
21.8.1 Introduction
21.8.2 Effect of Cultivation Media
21.8.3 Physical Parameters: pH, Temperature, and DO Control
21.8.4 Product Recovery and Downstream Processing
21.8.5 Solid-State Fermentation (SSF) and Submerged Fermentation (SMF)
21.8.6 CSTR Operations with Yeast
21.9 Conclusions
References
Index