New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Secondary Metabolites Biochemistry and Applications

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New and Future Developments in Microbial Biotechnology and Bioengineering: Microbial Secondary Metabolites
Biochemistry and Applications
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List of Contributors
1 Wild Mushrooms as Functional Foods: The Significance of Inherent Perilous Metabolites
	1.1 Introduction
	1.2 Mushroom and Its Taxonomy
	1.3 The Toxins and Their Perilous Connections
	1.4 Prospects and Concerns in Terms of Human Health
	1.5 Mushrooms as Dietary Supplements
	1.6 Protein Composition
	1.7 Lipid Composition
	1.8 Carbohydrates and Fiber content
	1.9 Mineral Composition
	1.10 Conclusion
	References
2 Genetic Manipulation of Secondary Metabolites Producers
	2.1 Introduction
	2.2 Genetic Engineering of the Secondary Metabolic Pathway in Plants
		2.2.1 Flavonoids and Anthocyanins: Biosynthesis and Regulatory Genes
		2.2.2 Alkaloids
			2.2.2.1 Crystalline and Nitrogenous Compounds: Biogenesis and Regulatory Factors
			2.2.2.2 Isoquinoline of Nitrogenous Organic Compounds of Plant
			2.2.2.3 Tropane Alkaloids and Pyrrolidine Alkaloids
		2.2.3 Terpenoids
			2.2.3.1 The essential oils of plants and simple derivatives
			2.2.3.2 Carotenoids
		2.2.4 Carboxybenzene Formatives
			2.2.4.1 Phytoanticipins (α-Hydroxynitrile-Type Aglycone and of a Sugar Moiety)
	2.3 Secondary Metabolites in Actinomycetes by Metabolic Engineering
		2.3.1 Precursor Engineering of Carbohydrate and Fatty Acid Metabolism
		2.3.2 Technology Regulating Systems
		2.3.3 Engineering Biosynthetic Structural Genes
	2.4 The Aspergillus nidulans MAPK Module and Secondary Metabolism
		2.4.1 Development Modular Controls
			2.4.1.1 MAP Kinase Module for Secondary Metabolite Synthesis
	2.5 Conclusions and Future Scope
	Acknowledgment
	References
3 Role of Rhizobacterial Secondary Metabolites in Crop Protection Against Agricultural Pests and Diseases
	3.1 Introduction
	3.2 Early Uses of Biocontrol Methods in Agriculture
	3.3 Microbial Secondary Metabolites
	3.4 Rhizobacterial Secondary Metabolites and Biological Control
		3.4.1 Antibiotics
			3.4.1.1 Water-Soluble Antibiotics
			3.4.1.2 Microbial Volatile Organic Compounds
				3.4.1.2.1 Antifungal Activity
				3.4.1.2.2 Antibacterial Activity
				3.4.1.2.3 Nematicidal Activity
				3.4.1.2.4 Insecticidal Activity
		3.4.2 Iron Sequestering
		3.4.3 Chemical Communication Interference
		3.4.4 Priming of Induced Systemic Resistance
	3.5 Regulation of Secondary Metabolites’ Production
		3.5.1 Regulation by Root Exudates Composition
		3.5.2 Regulation by Microbial Signals (Quorum-Sensing Signals)
	3.6 Microbial Metabolites and Biopesticides Development
	3.7 Concluding Remarks
	References
4 Bioengineering of Secondary Metabolites
	4.1 Introduction
	4.2 Gene Duplication in Idiophase
	4.3 Evolution of New Pathways
	4.4 Bioengineering of Terpenoids in Plants
	4.5 Metabolic Engineering and Microbial Biogenesis of Plant Isoprenoids
	4.6 Enzyme Engineering
	4.7 Conclusion
	Acknowledgment
	References
	Further Reading
5 Advances in Microbial Technology for Upscaling Sustainable Biofuel Production
	5.1 Introduction
	5.2 Biomass Feedstocks for Biofuels Production
	5.3 Downside of First- and Second-Generation Biofuels
	5.4 Metabolic Engineering and Biofuel Production
	5.5 Metabolic Pathways for Alcohol-Derived Fuels
	5.6 Metabolic Pathways for Isoprenoid-Derived Fuels
	5.7 Metabolic Pathways for Fatty Acid-Derived Fuels
	5.8 Synthetic Biology and Its Role in Design of Microbial Cell Factories
	5.9 Engineering Microbes for Tolerance to Next-Generation Biofuels
	5.10 Conclusion
	References
6 Bioprospecting Actinobacteria for Bioactive Secondary Metabolites From Untapped Ecoregions of the Northwestern Himalayas
	6.1 Introduction to Secondary Metabolites
	6.2 Introduction to Actinobacteria
	6.3 Distribution of Actinobacteria
	6.4 Choice of Actinobacteria as Source of Bioactive Secondary Metabolites
	6.5 Actinobacteria From Unusual Environments
	6.6 Northwestern Himalayas as Sources of Bioactive Actinobacteria
	6.7 Conclusion
	Acknowledgment
	References
7 Microbial Metabolites: Peptides of Diverse Structure and Function
	7.1 Introduction
	7.2 Antimicrobial Peptides
	7.3 Classification of Microbial AMPs
		7.3.1 Class I: Posttranslationally Modified Bacteriocins
			7.3.1.1 Class Ia: The Lantibiotics
			7.3.1.2 Class Ib: The Labyrinthopeptins
			7.3.1.3 Class Ic: The Sactibiotics
		7.3.2 Class II: Unmodified Bacteriocins
			7.3.2.1 Class IIa: The Pediocin-Like Bacteriocins
			7.3.2.2 Class IIb: The Two-Peptide Bacteriocins
			7.3.2.3 Class IIc: The Circular Bacteriocins
			7.3.2.4 Class IId: The Nonpediocin, Unmodified, Linear Bacteriocins
	7.4 Mechanism of Action
	7.5 Potential Applications of AMPs
	7.6 Conclusion
	References
	Further Reading
8 Agrobacterium rhizogenes Mediated Hairy Root Cultures: A Promising Approach for Production of Useful Metabolites
	8.1 Introduction
	8.2 Agrobacterium and Ri T-DNA Genes
	8.3 Role of rol Genes
	8.4 Secondary Metabolite Production
	8.5 Large-Scale Production of Hairy Roots
	8.6 Liquid-Phase Bioreactors
		8.6.1 Stirred Tank Reactor
		8.6.2 Airlift Bioreactors
		8.6.3 Bubble Column Reactor
		8.6.4 Convective Flow Reactor
		8.6.5 Turbine Blade Reactor
		8.6.6 Rotating Drum Bioreactor
	8.7 Gas Phase Bioreactors
	8.8 Hybrid Bioreactors
	8.9 Parameters That Affect Productivity
	8.10 Conclusion and Future Prospects
	References
9 Unleashing Extremophilic Metabolites and Its Industrial Perspectives
	9.1 Introduction
	9.2 Marine Microbial Metabolites Derived From Benthic Environment
	9.3 Marine Sponge—Microbial Symbionts
	9.4 Stromatolites: Potential Novel Source for Future Biotechnology
	9.5 Polyhydroxyalkanoate-Producing Free-Living Marine Bacteria
		9.5.1 Chemical Composition and Material Properties of Polyhydroxyalkanoates
	9.6 Stress Acclimatization of PHA-Producing Bacteria
	9.7 Production of Polyhydroxyalkanoate by Halophilic Bacteria
	9.8 Role of PHA Synthase in Halophiles
	9.9 Concluding Remarks
	References
	Further Reading
10 Hybrid Bioactive Products and Combinatorion Biosynthesis
	10.1 Introduction
	10.2 Need of Combinatorial Biosynthesis
	10.3 Precursor-Directed Combinatorial Biosynthesis
	10.4 Enzyme-Level Combinatorial Biosynthesis
		10.4.1 Site-Specific Mutagenesis
		10.4.2 Directed Evolution
	10.5 Pathway-Level Combinatorial Biosynthesis
	10.6 Conclusion
	Acknowledgment
	References
11 Rubromycins: A Class of Telomerase Inhibitor Antibiotics Produced by Streptomyces spp.
	11.1 Introduction
	11.2 Telomeres, Telomerase, and Cancer
	11.3 Rubromycins: A Class of Molecules Telomerase Activity Inhibition
	11.4 Mode of Action of Rubromycins Human Telomerase Inhibition
	11.5 Streptomyces spp.: The Biofactories for Human Telomerase Inhibitors Production
	11.6 Biosynthesis of Rubromycins
	11.7 Bioprocess of Rubromycins Production
		11.7.1 Future Perspectives
	References
12 Regulation by Metal Ions
	12.1 Introduction
	12.2 Regulatory Mechanisms
	12.3 Role of Specific Molecules in Controlling Biosynthetic Pathways
		12.3.1 Metal Ions in the Synthesis of Antimicrobial Agents
	12.4 Metal Ions in the Synthesis of Organic Acids
	12.5 Metal Ions in the Synthesis of Siderophores
	12.6 Metal Ions in the Synthesis of Microbial Pigments
	12.7 Metal Ions in the Synthesis of Vascular Permeability Factor
	12.8 Metal Ions in the Synthesis of Hydrogen Cyanide
	12.9 Conclusion
	References
13 Citric Acid Cycle Regulation: Back Bone for Secondary Metabolite Production
	13.1 History
	13.2 Citric Acid Cycle: Process and Regulation
		13.2.1 Synthesis of Citrate
		13.2.2 Isomerization of Citrate Into Isocitrate
		13.2.3 Conversion of Isocitrate Into α-Ketoglutarate
		13.2.4 Conversion of α-Ketoglutarate Into Succinyl CoA
		13.2.5 Conversion of Succinyl CoA Into Succinate
		13.2.6 Conversion of Succinate Into Fumarate
		13.2.7 Conversion of Fumarate Into Malate
		13.2.8 Conversion of Malate Into Oxaloacetate
		13.2.9 Citric Acid Cycle Enzymes as Multienzyme Complex
	13.3 Citric Acid Cycle as Biosynthetic Precursors
		13.3.1 Anaplerosis and Cataplerosis for Citric Acid Cycle Regulation
		13.3.2 Flux Modes of Citric Acid Cycle in Plants
		13.3.3 Flux Modes of Citric Acid Cycle in Bacteria
	13.4 Example of Synthesis of Metabolites Through Intermediates of Citric Acid Cycle
		13.4.1 Enhancement in the Production of Cellulose
		13.4.2 Enhancement of Fatty Acid Biosynthesis and Lipstatin Production
		13.4.3 Synthesis of Amino Acid
		13.4.4 Production of Citric Acid
		13.4.5 Production Itaconic Acid
		13.4.6 Production of Pyrimidines and Purines
		13.4.7 Production of 1,4 Butanediol
	13.5 Conclusion
	References
14 Resistance in Pathogenic Microorganisms
	14.1 Resistance in Bacteria
		14.1.1 Biochemistry of Resistance in Bacteria
			14.1.1.1 Antibiotic Inactivation
			14.1.1.2 Target Modification
			14.1.1.3 Alteration in Peptidoglycan Structure
			14.1.1.4 Interference in Protein Synthesis
			14.1.1.5 DNA Synthesis Interference
			14.1.1.6 Efflux Pumps and Permeability of Outer Membrane
	14.2 Resistance in Fungi
	14.3 Antifungal Resistance From Environmental Origin
	14.4 Resistance in Viruses
	References
15 Hybrid Approach for Transformation for Betulin (an Anti-HIV Molecule)
	15.1 Background of Betulin
	15.2 Main Sources of Triterpenes
	15.3 Applications
	15.4 Value Addition Using the Hybrid Approach
	15.5 Key Strategies for Adding Value
	15.6 Hybrid Approach to Develop Betulin Derivatives
	15.7 Issues in Chemical Synthesis
	15.8 Conclusion
	Acknowledgments
	References
	Further Reading
16 Producers of Bioactive Compounds
	16.1 Introduction
	16.2 Bioactive Compounds
	16.3 Major Classes of Bioactive Compounds
	16.4 Criteria for the Selection of an Ideal Bioactive Compound
	16.5 Diverse Biological Activities of Bioactive Compounds
	16.6 Sources of Bioactive Compounds
	16.7 Plants as the Sources of Bioactive Compounds
	16.8 Invertebrates as the Sources of Bioactive Compounds
	16.9 Microbial Producers of Bioactive Compounds
	16.10 Bacteria as Producers of Bioactive Compounds
	16.11 Fungi as Producers of Bioactive Compounds
	16.12 Algae as Producers of Bioactive Compounds
	16.13 Conclusion
	References
17 Bioremediation of Organic and Inorganic Pollutants Using Microalgae
	17.1 Introduction
	17.2 Inorganic Pollutants
		17.2.1 Heavy Metals
		17.2.2 Radioactive Compounds
	17.3 Organic Pollutants
		17.3.1 Petroleum Hydrocarbons and Polycyclic Aromatic Hydrocarbons
		17.3.2 Fertilizers and Pesticides
		17.3.3 Dimethyl Phthalate
		17.3.4 Tributyltin
		17.3.5 Explosives
	17.4 Role of Biosurfactants in the Bioremediation
	17.5 Emerging Pollutants
		17.5.1 Polyfluorinated Compounds
		17.5.2 Pharmaceutical Active Compounds
	17.6 Conclusion
	References
	Further Reading
18 Secondary Metabolites From Endophytic Fungi and Their Biological Activities
	18.1 Introduction
	18.2 Endophytic Fungal Diversity
	18.3 Secondary Metabolites
		18.3.1 Antibacterials/Antimycobacterials From Endophytic Fungi
		18.3.2 Antifungals From Endophytic Fungi
		18.3.3 Anticancer, Immunosuppressive, and Antiinflammatory Activities of Endophytic Fungi
		18.3.4 Antioxidants From Endophytic Fungi
		18.3.5 Industrial Enzymes From Endophytic Fungi
	18.4 Conclusions
	References
19 Regulation and Role of Metal Ions in Secondary Metabolite Production by Microorganisms
	19.1 Introduction
	19.2 Manganese
	19.3 Copper
	19.4 Nickel
	19.5 Calcium
	19.6 Cadmium
	19.7 Zinc
	19.8 Cobalt
	19.9 Iron
	19.10 Rare-Earth Elements
	19.11 Other Metals
	19.12 Conclusion and Future Prospect
	References
	Further Reading
20 Metabolic Engineering to Synthetic Biology of Secondary Metabolites Production
	20.1 Introduction
	20.2 Secondary Metabolites-Producing Microbes
	20.3 Discovery of Novel Microbes Producing Secondary Metabolites
	20.4 The Functional Genomics of Secondary Metabolites-Producing Microbes
	20.5 Biodiversity of Secondary Metabolites-Producing Microbes
		20.5.1 Plant-Associated Microbiomes
		20.5.2 Microbiomes From Extreme Habitats
			20.5.2.1 Psychrophilic Microbes
			20.5.2.2 Thermophilic Microbes
			20.5.2.3 Halophilic Microbes
	20.6 Distributions of Secondary Metabolites-Producing Microbes
		20.6.1 Archaea
		20.6.2 Bacteria
		20.6.3 Fungi
	20.7 Synthetic Biology for Secondary Metabolites Production
		20.7.1 Anthraquinones
		20.7.2 Quinones
		20.7.3 Phenolic Compounds
		20.7.4 Terpenoids
		20.7.5 Polyketides and Lactones
		20.7.6 Pyrones and Polyenes
		20.7.7 Alkaloids
		20.7.8 Immunosuppressive Compounds
	20.8 Biotechnological Applications of Secondary Metabolites
	20.9 Conclusion and Future Prospects
	Acknowledgment
	References
21 Microbial Enzymes as Control Agents of Diseases and Pests in Organic Agriculture
	21.1 Introduction
	21.2 Production of Microbial Enzymes
		21.2.1 Phases of a Fermentative Process to Obtain Enzymes
			21.2.1.1 Selection and Preparation of Inoculum
			21.2.1.2 Fermentation Process
				21.2.1.2.1 Solid-state fermentation
				21.2.1.2.2 Submerged Fermentation
	21.3 Enzyme Purification
	21.4 Role of Enzymes in Inducing Plant Resistance to Insect Attack
	21.5 Antioxidant Enzymes
	21.6 Types of Enzymes and Their Application in Agriculture for Pest Control
		21.6.1 β-1,3-Glucanase
		21.6.2 Pectinase
		21.6.3 Protease
		21.6.4 Lipase
		21.6.5 Chitinase
	21.7 Final Conclusion
	References
	Further Reading
22 Secondary Metabolites: Metabolomics for Secondary Metabolites
	22.1 Introduction
	22.2 Secondary Metabolites and Synthetic Biology
	22.3 Primary Metabolites
	22.4 Secondary Metabolite
	22.5 Genome and Genomics
		22.5.1 Transcriptome and Transcriptomics
	22.6 Proteome and Proteomics
		22.6.1 Metabolome and Metabolomics
	22.7 Synthetic Biology
	22.8 Metabolomics and Synthetic Biology: How to Engineer the Microbes
	22.9 Discovery of Secondary Metabolites: How to Discover Secondary Metabolites Through Metabolomics
	22.10 Production of Secondary Metabolites
	22.11 Role of Metabolomics in Identification of the Bottleneck in Engineered Pathway
	22.12 Conclusion and Future Perspectives
	Acknowledgments
	Conflict of Interest
	References
23 Solid-State Fermentation Strategy for Microbial Metabolites Production: An Overview
	23.1 Introduction
	23.2 History of SSF
	23.3 Common Characteristics of Solid-State Fermentation
	23.4 Analysis of Substrate Selection for Solid-State Fermentation
	23.5 Microorganisms and Growth Kinetics for Solid-State Fermentation
	23.6 Physicochemical Parameters for Solid-State Fermentation
	23.7 Bioreactor for the Solid-State Fermentation
	23.8 Conclusion
	Acknowledgement
	References
Index
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