Actinobacteria: Microbiology to Synthetic Biology

Foreword
Preface
Contents
Contributors
Chapter 1: Actinomycetes: Microbiology to Systems Biology
	1.1 Introduction to Actinobacteria
	1.2 Classification and Taxonomy of Actinobacteria
	1.3 Habitats of Actinobacteria
		1.3.1 Actinobacteria from Terrestrial Habitat
		1.3.2 Actinobacteria from Aquatic Habitat
		1.3.3 Actinobacteria as a Symbiont
	1.4 Distribution of Bioactive Compounds in Actinobacteria
	1.5 Potential Avenues in Actinomycetes Research
		1.5.1 Drug Leads Research in Actinobacteria
			1.5.1.1 β-Lactamases in Actinobacteria
			1.5.1.2 Polyketides and Non-ribosomal Peptides
			1.5.1.3 Isoprenoids
			1.5.1.4 Indolocarbazoles
			1.5.1.5 Prodiginines
			1.5.1.6 Antimicrobial Enzymes from Actinobacteria
			1.5.1.7 Antiviral Compounds from Actinobacteria
			1.5.1.8 Antitumor Enzymes from Actinobacteria
			1.5.1.9 Fibrinolytic Enzymes from Actinobacteria Spp.
		1.5.2 Actinobacteria in Treating Skin Diseases
	1.6 Industrially Important Biomolecules from Actinobacteria
		1.6.1 Hydrolytic Enzymes
			1.6.1.1 Amylases
			1.6.1.2 Cellulase, Endoglucanases, and Xylanases
			1.6.1.3 Lipases
			1.6.1.4 Laccase
			1.6.1.5 Alkaline Proteases and Keratinase
			1.6.1.6 Pectinases
	1.7 Current Trends Explore the Actinomycete Storehouse
		1.7.1 Genomic Analysis
		1.7.2 Genome Mining
		1.7.3 Genome Scanning
		1.7.4 Systems Biology and Biotechnology of Streptomyces Species
	1.8 Conclusion
	References
Chapter 2: Diversity of Actinobacteria in Various Habitats
	2.1 Introduction
	2.2 Actinobacterial Diversity in Soil
	2.3 Actinobacterial Diversity in Saline Environment
	2.4 Actinobacterial Diversity in Rhizosphere
	2.5 Actinobacteria as Endophytes
	2.6 Actinobacterial Diversity in Marine Environment
	2.7 Actinobacterial Diversity in Terrestrial Hot Springs, Volcanic and Geothermal Soil
	2.8 Actinobacterial Diversity in Deserts and Arid Regions
	2.9 Conclusion
	References
Chapter 3: Traditional Screening and Genome-Guided Screening of Natural Products from Actinobacteria
	3.1 Introduction
	3.2 Traditional Approaches
		3.2.1 Phenotypic Assay
			3.2.1.1 Rare Actinomycetes as a Potential Source for New Bioactive Compounds
			3.2.1.2 Exploring for New Isolates in Diverse Natural Habitats
			3.2.1.3 Combined Culture (Co-Cultivation) Technique to Induce Secondary Metabolite Production
		3.2.2 Chemical Structure-Based Screening
	3.3 Genetic Tools for Screening for Novel Bioactive Compounds
		3.3.1 Whole Genomic Sequencing
		3.3.2 Metagenomics Technique
		3.3.3 CRISPR/Cas 9 for Discovery New Natural Products
	3.4 Conclusion
	References
Chapter 4: The Relationship between Actinobacteria and Rice
	4.1 Introduction
	4.2 Biodiversity of Actinobacteria from Jasmine Rice (O. Sativa)
	4.3 Actinobacterial Endophytes in Rice
	4.4 Actinobacteria as Biological Control agents Against Rice Pathogens
	4.5 Actinobacteria Beneficiate Rice Growth by Synthesis of Protein
	4.6 Actinobacteria as Rice Pathogens
	4.7 Prospect of Rice Actinobacteria
	References
Chapter 5: Nonribosomally and Ribosomally Synthesized Bioactive Peptides (NRPS and RiPPs) from Actinobacteria
	5.1 Introduction
	5.2 Nonribosomal Peptides in Actinobacteria
		5.2.1 NRPS Gene Clusters Attributed to Bioactivity
	5.3 Methods for Discovering Nonribosomal Peptides: Proteomic Approach
		5.3.1 NRPquest
		5.3.2 Pep2Path
	5.4 Ribosomally Synthesized and Post-Translationally Modified Peptides-Lantipeptides
		5.4.1 Biosynthetic Machinery
		5.4.2 Classes of Lantipeptides
			5.4.2.1 Class I
			5.4.2.2 Class II
			5.4.2.3 Class III
			5.4.2.4 Class IV
	5.5 Generic Lantipeptides of Actinobacteria and Applications
	5.6 Tools for Identification of Lantipeptides
		5.6.1 BAGEL3
	References
Chapter 6: Genome Data Mining, Chemistry and Bioactivity of Sesquiterpenes from Actinobacteria
	6.1 Introduction
	6.2 Chemistry of Sesquiterpenes
	6.3 Biosynthesis of Sesquiterpenes from Actinobacteria
	6.4 Genome Mining of Sesquiterpene from Actinobacteria
	6.5 Future Perspectives
	References
Chapter 7: Mining for Biosynthetic Gene Clusters in Actinobacteria Genomes Via Bioinformatics Tools
	7.1 Introduction
	7.2 Next-Generation Sequencing
	7.3 Metagenomic Assembly
	7.4 Gene Prediction and Annotation
	7.5 Secondary Metabolite Biosynthetic Gene Clusters
	7.6 In Silico Tools for Genome Mining of smBGCs
	7.7 Characterizing smBGCs Identified by Genome Mining
	7.8 PK and NRP Biosynthetic Pathways Detection Using Bioinformatics Tools
	7.9 Detection of Unique Gene Clusters
	7.10 Phylogenetic Binning
	7.11 Conclusion
	7.12 Future Perspectives
	References
Chapter 8: Cloning and Heterologous Expression of Natural Products from Actinobacteria
	8.1 Introduction
	8.2 Identification of BGCs for Known Natural Products
	8.3 Conventional Expression Systems
		8.3.1 Genomic Libraries
			8.3.1.1 Isolation of High-Quality DNAs
			8.3.1.2 DNA Fragmentation
			8.3.1.3 Cloning
		8.3.2 Integrase-Mediated Site-Specific Recombination (ISR)
		8.3.3 Linear-Linear Homologous Recombination (LLHR)
		8.3.4 Transformation-Associated Recombination (TAR): The Solution for Cloning Large NP BGCs
	8.4 Technical Advancements in Heterologous Expression of BGCs
	8.5 Application of Heterologous Expression Systems
		8.5.1 Novel Compound Discovery Through Heterologous Expression of BGCs
			8.5.1.1 Cryptic BGC Expression
			8.5.1.2 Recombineering Techniques
		8.5.2 Novel Compound Discovery Through Heterologous Expression of Metagenomic DNA
	8.6 Concluding Remarks
	References
Chapter 9: Synthetic Biology and Metabolic Engineering in Actinobacteria for Natural Product Production
	9.1 Introduction
	9.2 An Overview of Engineering in Actinobacteria for Natural Products (NPs) Overproduction
	9.3 Recent Advances in Metabolic Engineering in Actinobacteria
		9.3.1 CRISPR Technology
		9.3.2 Other Newly Developed Techniques and Tools
	9.4 Advantages of Actinobacteria as a Host for Metabolic Engineering
	9.5 Concluding Remarks and Future Perspectives
	References
Chapter 10: CRISPR ERA: Current Applications and Future Perspectives on Actinobacteria
	10.1 Introduction
		10.1.1 Biosynthetic Gene Clusters and Natural Products
		10.1.2 Actinomycetes Phyla as a Source of Bioactive Compound
	10.2 CRISPR/CAS-Based Gene Editing Strategies in Streptomyces
		10.2.1 Nuclease-Dependent Editing System
		10.2.2 CRISPRi and CRISPRa-Based Genome Editing
		10.2.3 CRISPR/Cas9: Knock-in Strategy
		10.2.4 CAPTURE Method
		10.2.5 CRISPR-BEST
		10.2.6 CAT-Fishing
	10.3 CRISPR/CAS Systems in Other Actinomycetes
		10.3.1 Gardnerella spp.
		10.3.2 Salinispora
		10.3.3 Nonomuraea sp.
	10.4 Application of CRISPR/Cas Systems In Biotechnology
	10.5 CRISPR Cas 3 Genes from Actinobacteria
	10.6 Future Perspectives
	References
Chapter 11: Uncultured Actinobacteria and Reverse Engineering and Artificial Intelligence Role in Future
	11.1 Introduction
		11.1.1 Boom of Actinobacterial Taxonomy
	11.2 Actinobacterial Reverse Engineering
	11.3 Machine Learning and Artificial Intelligence Approach
		11.3.1 Digital Microbiological Image Technology
	11.4 Future Perspectives
	11.5 Conclusion
	References
Chapter 12: Cultivation and Diversity of Marine Actinomycetes: Molecular Approaches and Bioinformatics Tools
	12.1 Introduction
	12.2 Cultivation Strategies and Diversity of the Marine Actinomycetes
		12.2.1 Traditional Techniques
		12.2.2 High-Throughput Cultivation Techniques
			12.2.2.1 Extinction Culturing
			12.2.2.2 Encapsulation of Single Cells
			12.2.2.3 Diffusion Chambers, Isolation Chips, and Microbial Traps
	12.3 Phylogenetic and Phenotypic Analysis of the Marine Actinomycetes
	12.4 Metagenomics and Metabolomics Approaches for the Analysis of Microbial Diversity
		12.4.1 Metagenomics Approach
		12.4.2 Metabolomics Approach
	12.5 Marine Actinobacteria: Diversity, Molecular Signature/s, and Bioinformatics Tools
	References
Chapter 13: Antimicrobial Potential and Metabolite Profiling of Marine Actinobacteria
	13.1 Introduction
	13.2 Antibiotics: Past and Present
		13.2.1 Antibiotics from Actinomycetes: Research and Developments
		13.2.2 Marine Actinomycetes: The Source of Novel Antimicrobial Compounds
			13.2.2.1 Bioactive Compounds from Marine Actinomycetes with Novel Pharmaceutical Potential
	13.3 Metabolite Profiling of Marine Actinobacteria
		13.3.1 Antibacterial Activities
			13.3.1.1 Antibacterial Compounds from Marine-Derived Streptomyces sp.
			13.3.1.2 Antibacterial Compounds from Marine-Derived NOCARDIOPSIS sp.
			13.3.1.3 Antibacterial Compounds from Marine-Derived Micromonospora sp.
			13.3.1.4 Antibacterial Compounds from Other Marine-Derived Actinomycetes
		13.3.2 Antifungal Activities
		13.3.3 Anticancer Activities
		13.3.4 Antitumor Activities
	13.4 Conclusion
	References
Chapter 14: Pharmacology of FDA-Approved Medicines from Actinobacteria
	14.1 Introduction
	14.2 Tigecycline
	14.3 Everolimus
	14.4 Telithromycin
	14.5 Miglustat
	14.6 Daptomycin
	14.7 Amrubicin
	14.8 Biapenem
	14.9 Ertapenem
	14.10 Pimecrolimus
	14.11 Gemtuzumab
	14.12 Summary
	References