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