Biomanufacturing for Sustainable Production of Biomolecules

Foreword
Preface
Acknowledgment
Contents
Editors and Contributors
1: Strain Design and Optimization Methods for Sustainable Production
1.1 Introduction
1.2 Strain Design and Development
1.2.1 Concept
1.2.2 Methods and Tools
1.2.2.1 Chassis Selection
1.2.2.2 Pathway Implementation
1.2.3 Rewiring the Cell and Production Optimization
1.3 Success Stories
1.3.1 E. coli Cell Factories on the Horizon
1.3.2 An Explorative Journey into Yeast Platform Strains
1.3.3 Fungi as Cell Factories
1.3.4 Towards Mammalian Cell Factories
1.4 Perspectives
References
2: Minimal Cells and Genome Minimization: Top-Down and Bottom-Up Approaches to Construct Synthetic Cells
2.1 Genome Minimization
2.1.1 Construction of a Minimal Genome
2.1.1.1 Top-Down Approach for Genome Minimization
2.1.1.2 Bottom-Up Approach for Genome Minimization
2.1.2 Essential and Non-essential Genes
2.1.2.1 Essential Genes
2.1.2.1.1 Transposon Mutagenesis
2.1.2.1.2 Antisense RNA
2.1.2.1.3 Systematic Inactivation of Genes
2.1.2.2 Non-essential Genes
2.1.3 Minimal Genomes
2.1.3.1 Bacterial Genome Minimization
2.1.3.1.1 E. coli
2.1.3.1.2 Mycoplasma
2.1.3.1.3 B. subtilis
2.1.3.2 Yeast
2.1.4 Naturally Occurring Minimal Genomes
2.1.5 Applications of Minimal Genomes
2.1.6 Limitations of Genome Minimization
2.2 Synthetic Minimal Cells
2.2.1 Membrane
2.2.1.1 GUVs
2.2.1.2 Proteinosomes
2.2.1.3 Polymersomes
2.2.2 RNA Cell
2.2.3 Cell-Matrix-Cell Dynamics
2.2.4 Synthetic Cell Communication
2.2.5 Energy Currency
2.3 Conclusion
References
3: Recent Advances in Downstream Processing Deployed in the Treatment of Pharmaceutical Effluents
3.1 Introduction
3.2 Pharmaceutical Wastewater
3.2.1 The Sources of Pharmaceutical Waste
3.2.2 Requirement of Effluent Treatment Linked with Pharmaceutical Waste
3.2.3 Treatment of Wastewater
3.3 Current Approaches in Downstream Processing Related to Treatments of Pharmaceutical Wastewater
3.3.1 Coagulation and Sedimentation
3.3.2 Flotation
3.3.3 Absorption of Activated Charcoal
3.4 Emerging Treatment Processes
3.4.1 Advanced Oxidation Processes
3.4.1.1 Application of AOPS
3.4.2 Wet Air Oxidation (WAO)
3.4.2.1 Wet-Air Oxidation Industrial Applications
3.4.3 Supercritical Water Oxidation (SCWO)
3.4.3.1 Application of Supercritical Water Oxidation
3.4.4 Photocatalysis
3.4.4.1 Advantages of Photocatalysis
3.5 Conclusion
References
4: Microbial Conversion of Waste to Biomolecules
4.1 Introduction
4.1.1 Waste for Biomolecule Production
4.1.1.1 Food Waste
4.1.1.2 Lignocellulosic Biomass
4.1.1.3 Municipal Solid Waste
4.2 Microbial Conversion of Waste by Microorganism
4.2.1 Introduction to Microbial Conversion
4.2.2 Biowaste to Biomolecules
4.2.2.1 Biowaste Conversion to Biomolecules from Plant Origin
4.2.2.1.1 Polysaccharides
4.2.2.1.2 Lactic Acids
4.2.2.1.3 Pectins
4.2.2.2 Biowaste Conversion to Biomolecules from Animal Origin
4.2.2.2.1 Hydroxyapatite
4.2.2.2.2 Collagen
4.2.2.2.3 Biohydrogen
4.3 Potential and Challenges of Microbial Conversion of Waste
4.3.1 Potential Solution to Environmental Concern on Waste Management
4.3.2 Waste as Feedstock for Bioeconomy
4.3.3 Sustainable Production of Value-Added Product
4.3.4 Challenges to Microbial Conversion of Waste
4.4 Conclusion
References
5: Biosensor for Detecting Biomolecules
5.1 Introduction
5.2 Concept
5.2.1 Principles of Optical Biosensors
5.2.2 Principles of Electrochemical Biosensors
5.2.3 Principles of Thermal Biosensors
5.2.4 Principles of Piezoelectric Biosensors
5.3 Biosensor Design: Materials, Fabrication, and Modification
5.3.1 Acetylcholinesterase Inhibition-Based Biosensors
5.3.2 Microalgae Biosensors
5.3.3 Yeast-Based Biosensors
5.3.4 Nanomaterial-Based Biosensors
5.3.5 Microbial Fuel Cell-Based Biosensors
5.4 Recent Advances in Biosensor Technology
5.4.1 Functionalization of Sensing Material
5.4.2 Configuration of Porous Detection Platform to Ease the Sensing Activities
5.4.3 Development of Biosensor for COVID-19 Detection
5.5 Conclusions, Future Prospects, and Challenges
References
6: Artificial Intelligence-Assisted Production of Biomolecules
6.1 Introduction
6.2 Machine Learning in Production of Biomolecules
6.3 Deep Learning in the Production of Biomolecules
6.4 Polymeric Biomaterial Applications Using Machine Learning
6.5 Self-Assembled Dipeptide Hydrogels Using Machine Learning
6.6 Response of Cell and Adsorption of Proteins on Polymeric Surfaces Using Machine Learning
6.7 Prediction of Protein Structure Using Deep Learning
6.8 Emerging Trends in ML-Based Enzyme Engineering Approaches
6.9 Artificial Intelligence-Assisted Ultrasonic Extraction of Flavonoids
6.10 Biological Data Interpretation and Integration with Other Omic
6.11 NMR Databases and Software for Metabolite Identification
6.12 Automated Structural Classification of Lipids Using Machine Learning
6.13 AI Research on the Production of Nutrient Biomolecules
6.14 Summary
References
7: Escherichiacoli Cell Factory for Synthesis of Biomolecules
7.1 Introduction
7.2 Metabolic Engineering of Escherichia coli
7.2.1 Central Metabolism
7.2.2 Production of Ethanol
7.2.3 Production of Acetate
7.2.4 Production of Lactate
7.2.5 Production of Succinate
7.3 Optimisation for the Production of Bioactive Compounds
7.3.1 Precursor Pools
7.3.2 Cofactor Levels
7.3.3 Gene Expression Balancing Levels
7.3.4 Substrate Channelling
7.3.5 Pathway Modularisation
7.4 Bioactive Compounds from E. coli
7.4.1 Organic Acids
7.4.2 Biodiesels
7.4.3 Polyhydroxyalkanoates
7.4.4 Hydrogen
7.4.5 Flavour and Fragrance
7.5 Future, Advances and Applications
7.6 Conclusion
References
8: Bacillus subtilis Cell Factory
8.1 Introduction
8.2 Bacillus subtilis Cell Factory for Vitamin Production
8.3 Bacillus subtilis Cell Factory in the Production of Industrially Important Enzymes
8.3.1 Amylase
8.3.2 Xylanases
8.3.3 Lichenase
8.4 Role of Bacillus subtilis in Terpenoid Biosynthesis
8.5 Genetic Engineering Tools and Strategies to Improve B. subtilis Cell Factory
8.6 Potential Application of Bacillus subtilis in Agriculture
References
9: Biomanufacturing for Sustainable Production of Biomolecules: Pseudomonas putida Cell Factory
9.1 Introduction
9.2 Cell Factory Engineering and Tolerance
9.2.1 Cell Genetic Tolerance
9.2.2 Optimal Flux Engineering
9.2.3 Biosurfactant Synthesis
9.2.4 Biofilm Cultivation
9.3 Metabolic Engineering Production
9.3.1 Rhamnolipids
9.3.2 Ethylene Glycol
9.3.3 Terpenoids
9.3.4 Polyketides and Non-ribosomal Peptides
9.4 Industrial Application
9.5 Conclusion
References
10: Cyanobacteria for Marine-Based Biomolecules
10.1 Introduction
10.2 An Outlook of Cyanobacteria Metabolites
10.3 Potentials of Cyanobacteria
10.3.1 Cyanobacteria Potential: Biofuel
10.3.2 Cyanobacteria Potential: Parasitic Nematodes Management
10.3.3 Cyanobacteria Potential: Nutraceutical
10.3.4 Cyanobacteria Potential: Biofertilizer
10.4 Biomolecules Diversity and Genetic Engineering of Cyanobacteria
10.4.1 Pigments
10.4.2 Carbohydrates
10.4.3 Protein
10.5 Medicinal and Clinical Applications
10.6 Sustainable Production of Cyanobacteria-Based Biomolecules
10.7 Overall Challenges in the Development of Cyanobacteria
10.8 Future Perspective
10.9 Summary
References
11: Yeast Cell Factory for Production ofBiomolecules
11.1 Introduction
11.1.1 Why Yeast Is Used as Cell Factory?
11.1.1.1 Methylotrophic Yeast
11.1.1.2 Non-methylotrophic Yeast
11.1.1.2.1 Saccharomyces cerevisiae
11.1.1.2.2 Pichia pastoris
11.1.1.2.3 Hansenula polymorpha
11.1.1.2.4 Yarrowia lipolytica
11.1.1.2.5 Kluyveromyces lactis
11.1.1.2.6 Schizosaccharomyces pombe
11.2 Tools and Strategies
11.2.1 Promoters as Tool
11.2.1.1 Structure of Yeast Promoters
11.2.1.1.1 Core Promoter Region
11.2.1.1.2 UAS and URS
11.2.1.1.3 Nucleosomes Disfavoring Sequences
11.2.1.2 Types of Promoters
11.2.1.3 Promoter Engineering
11.2.2 Native Promoters
11.2.3 Hybrid Promoters
11.2.4 Synthetic Promoters
11.2.4.1 Synthetic Promoters Controlled by Bacterial Proteins
11.2.4.1.1 Promoters Regulated by LexA
11.2.4.1.2 Promoters Regulated by TetR
11.2.4.1.3 Promoters Regulated by LacI
11.2.4.1.4 Promoters Regulated by XylR
11.2.4.2 Synthetic Promoters for Expanding Dynamic Ranges
11.2.4.3 Synthetic Promoters for Reducing Homologous Recombination
11.2.4.4 Synthetic Promoters with Minimal Size
11.2.4.5 Synthetic Promoters for Multi-host Application
11.2.4.6 Applications of Yeast Cell Factories
11.2.4.7 Biofuel Synthesis
11.2.4.8 Production of Virus-Like Particles (VLP)
11.2.4.9 Biomass Utilization
11.2.4.10 Synthesis of Fatty Acids and Derived Products
11.2.4.11 Pharmaceutical Protein Production
11.2.4.12 Genome Editing
11.2.4.13 Miscellaneous Applications
11.2.4.13.1 Yarrowia lipolytica as Cell Factory
11.2.4.13.2 Production of Lipids
11.2.4.13.3 Pichia pastoris as Cell Factory
11.2.4.13.4 Heterologous Protein Production
11.2.4.13.5 Production of Industrial Enzymes
11.2.4.13.6 Schizosaccharomyces pombe as Cell Factory
11.2.4.13.7 Kluyveromyces lactis as Cell Factory
11.3 Concluding Remarks
References
12: Plant Cell Factory for Production ofBiomolecules
12.1 Introduction
12.2 Production of Iron-Containing Biomolecules
12.2.1 Role of Transcription Factors in Equanimity of Iron
12.2.2 Classical and Traditional Avenue for Biofortifying Iron
12.2.3 How Hindrance of Iron Affects Plastids
12.2.4 Iron Deficiency-Induced Genes
12.3 In Vitro Culture of Varied Plant Species in the Production of Caffeoylquinic Acids CQAs and Their By-Products
12.3.1 Involvement of Shikimic Pathway in Synthesizing CQAs
12.3.2 CQAs Compound Isolation from Epiphytes
12.3.3 Quantitative and Qualitative Approaches for Identification
12.4 Biosynthesis of Zinc/ZnO-Containing Nanoparticles in Plants
12.4.1 Enhancing Attributes of Maize Plant Using ZnO Nanoparticles
12.4.2 Distinct Approaches for Forming Zinc NP Using Plant Extracts
12.4.3 Zn Nanoparticle in Regard to Toxicity
12.4.4 Effect of Zn NP on Mutagenicity of Barley
References
13: Genetic Manipulation of Crop for Enhanced Food Quality and Nutrition Toward Sustainable Production
13.1 Introduction
13.2 Improving Food Quality and Nutrition Through Plant Breeding
13.3 Chromosome and Embryo Manipulation
13.4 Transgenic Technologies
13.5 Potential of Genome Editing in Crop Improvement
13.6 Synthetic Biology for Future Agriculture and Nutrition
13.7 Application of Plant Biotechnology in Nutritional Therapy, Phytonutrients, and Phytotherapy
13.8 Conclusions and Future Remarks
References
14: Insect Cell Factory for Production of Biomolecules
14.1 Introduction
14.2 Insect Cells
14.3 Insect Cell Metabolism
14.4 By-products of Insect Cells
14.5 Vector for Insect Cell Infection
14.6 Cultivation of Insect Cells
14.7 Insect Cell-Baculovirus System Proteolysis
14.8 Screening Transformed Insect Cell Lines for Recombinant Protein Production
14.9 Potential for O-Glycosylation in Lepidopteran Insect Cell Lines
14.10 Post-translational Events and Protein Folding
14.11 Expression of Human Sialic Acid Pathway Gene in Insect Cells (Spodoptera frugiperda)
14.12 Enhanced Secreted and Membrane-Targeted Protein Expression in Insect Cells
References
15: Mammalian Cell Culture: An Edge to Biopharmaceutical Industry
15.1 Introduction
15.1.1 Current Situation of Mammalian Cell Culture Market
15.2 Market Size
15.3 Geographic Distribution of Cell Culture Capacity
15.4 Equipment Required for Mammalian Cell Culture
15.4.1 Cell Culture Process
15.4.1.1 Seed Train Expansion or Inoculum Train
15.4.1.2 Production Bioreactor
15.4.2 Bioreactor Types
15.4.2.1 Homogeneous System
15.4.2.1.1 Stirred Tank Bioreactor
15.4.2.1.2 Bubble Tank Bioreactor
15.4.2.1.3 Airlift Bioreactor
15.4.2.1.4 WAVE Bioreactor
15.4.2.1.5 Rocking Bioreactor
15.4.2.2 Heterogeneous System
15.4.2.2.1 Stirred Tank Bioreactor with Microcarriers
15.4.2.2.2 Fixed-Bed Bioreactor
15.4.2.2.3 Fluidized-Bed Bioreactor
15.4.2.2.4 Immobilized-Bed Bioreactor
15.4.2.2.5 Hollow-Fiber Bioreactor
15.4.3 Bioreactor Operation Modes
15.4.3.1 Batch Culture
15.4.3.2 Fed-Batch Culture
15.4.3.3 Continuous Culture
15.4.3.4 Repeated Fed-Batch/ Semicontinuous Culture
15.5 Approaches for Protein Expression
15.5.1 Internal Ribosome Entry Site (IRES)
15.5.2 Ubiquitous Chromatin Opening Element (UCOE)
15.5.3 Selection Marker Attenuation
15.5.4 Matrix Attachment Regions
15.5.5 Site-Specific Recombination
15.6 Conclusion
References
16: Genome Editing in the Synthetic Biology for Sustainable Production of Biomolecules
16.1 Introduction
16.2 Synthetic Biology Tools for Biomolecules Production
16.2.1 Conventional Genetic Engineering Techniques for Biomolecule Production
16.2.2 Genome Editing Based on CRISPR/Cas9 System
16.2.3 Mechanism of CRISPR/Cas9
16.3 Potential Advantages
16.3.1 Role in Gene Therapy
16.3.2 Therapeutic Role of CRISPR/Cas9
16.4 Disadvantages or Drawbacks of CRIPSR
16.4.1 Lack of Equipment
16.4.2 Lack of Assured Efficiency
16.4.3 Due to Off-Target Pairing
16.5 Genome Editing for the Production of High-Value Biomolecules
16.5.1 Genome Editing for Production of High-Value Biomolecules in Bacteria
16.5.2 Genome Editing for High-Value Production of Biomolecules in Yeast
16.5.3 Genome Editing for Production of High Value Biomolecules in Fungi
16.6 Summary
References
17: Cell-Free Systems for Sustainable Production of Biofuels
17.1 Introduction
17.2 Cell-Free System for Production of Ethanol
17.3 Cell-free System for Butanol Production
17.4 Cell-free System for Hydrogen Production
17.5 Production of Advanced Biofuels
17.5.1 Isoprene
17.5.2 Bisabolene
17.5.3 Limonene
17.5.4 Pinene
17.5.5 Sabinene
17.5.6 Farnesene
17.6 Conclusion and Future Remarks
References
18: Challenges and Opportunities in Biomanufacturing
18.1 Introduction
18.2 Biomanufacturing Revolutions
18.2.1 Premodern Biomanufacturing
18.2.2 Biomanufacturing 1.0
18.2.3 Biomanufacturing 2.0
18.2.4 Biomanufacturing 3.0
18.2.5 Emerging Biomanufacturing 4.0
18.3 Challenges and Opportunities in Biomanufacturing
18.3.1 Food and Beverage Biomanufacturing
18.3.2 Biomanufacturing in Tissue Engineering and Regenerative Medicine
18.3.3 Biomanufaturing of Medicines and Pharmaceuticals
18.3.4 Biomanufacturing of Therapeutic Cells
18.4 Concluding Remarks and Future Directions
References