Biomolecular Engineering Solutions for Renewable Specialty Chemicals

R. Navanietha Krishnaraj, PhD, is Research Professor in the Composite and Nanocomposite Advanced Manufacturing-Biomaterials Center in the Department of Chemical and Biological Engineering at the South Dakota School of Mines and Technology. He received the Award for Cutting Edge Research (Fulbright Faculty Award) in 2016. Rajesh K. Sani, PhD, is Professor in the Departments of Chemical and Biological Engineering at South Dakota School of Mines and Technology, South Dakota, USA. He is the Biocatalysis Program Committee Member for the Society for Industrial Microbiology and Biotechnology.

• Preface xviiList of Contributors xix1 Engineered Microorganisms for Production of Biocommodities 1Akhil Rautela and Sanjay Kumar1.1 Introduction 11.2 Fundamentals of Genetic Engineering 21.2.1 DNA-altering Enzymes 21.2.1.1 DNA Polymerases 41.2.1.2 Nucleases 41.2.1.3 Ligases 51.2.1.4 DNA-modifying Enzymes 61.2.2 Vectors 71.2.3 Incorporation of Modified DNA into Host 81.2.3.1 Introducing Recombinants into Prokaryotes 81.2.3.2 Introducing Recombinants into Eukaryotic Hosts 91.2.4 Selection of Transformants 101.2.4.1 Direct Selection 101.2.4.2 Identification of the Clone from a Gene Library 111.3 Beneficial Biocommodities Produced Through Engineered Microbial Factories 121.3.1 Biopolymers 131.3.1.1 Cellulose 141.3.1.2 Poly-ϒ- glutamic Acid 151.3.1.3 Hyaluronic Acid 161.3.1.4 Polyhydroxyalkoate 181.3.2 Organic Acids 201.3.2.1 Citric Acid 211.3.2.2 Lactic Acid 231.3.2.3 Succinic Acid 241.3.2.4 Fumaric Acid 261.3.3 Therapeutic Proteins 271.4 Photosynthetic Production of Biofuels 281.4.1 Biohydrogen 291.4.2 Biodiesel 301.4.3 Bioethanol 311.4.4 Terpenoids 321.5 Conclusion 34References 342 Microbial Cell Factories for the Biosynthesis of Vanillin and Its Applications 49Sukumaran Karthika, Manoj Kumar, Santhalingam Gayathri, Perumal Varalakshmi, and Balasubramaniem Ashokkumar2.1 Introduction 492.2 Natural Sources of Vanilla and Its Production 512.3 Biotechnological Production of Vanillin 522.3.1 Enzymatic Synthesis of Vanillin 522.3.2 Microbial Biotransformation of Ferulic Acid to Vanillin 542.3.3 Agro-wastes as a Source for Biovanillin Production 582.4 Strain Development for Improved Production of Vanillin 602.4.1 Metabolic and Genetic Engineering 602.5 Bioactive Properties of Vanillin 632.5.1 Antimicrobial Activity 632.5.2 Antioxidant Activity 632.5.3 Anticancer Activity 642.5.3.1 Apoptosis Pathway 642.5.3.2 Tumor Necrosis Factor-induced Apoptosis 642.5.3.3 Cell Cycle Arrest 652.5.3.4 Nuclear Factor κB (NF-κB) Pathway 652.5.4 Anti-sickling Activity 652.5.5 Hypolipidemic Activity 662.6 Conclusion 66Acknowledgments 66References 673 Antimicrobials: Targets, Functions, and Resistance 77Madhuri Dutta, Sinjini Patra, Shivam Saxena, and Anasuya Roychowdhury3.1 Introduction 773.2 Classification of Antibiotics 773.2.1 Classification of Antibiotics Based on Mode of Action: Bactericidal and Bacteriostatic 783.2.2 Classification of Antibiotics Based on the Spectrum of Action: Broad-and Narrow-spectrum Antibiotics 793.3 Antibacterial Agents 793.3.1 Penicillins 793.3.1.1 Mechanism of Action 823.3.1.2 Clinical Implications 833.3.2 Cephalosporins 833.3.2.1 Mechanism of Action 833.3.2.2 Clinical Indications 853.3.3 Macrolides 853.3.3.1 Mechanism of Action 853.3.3.2 Clinical Indications 853.3.4 Fluoroquinolones 863.3.4.1 Mechanism of Action 863.3.4.2 Clinical Indication 863.3.5 Sulfonamides 873.3.5.1 Mechanism of Action 873.3.5.2 Clinical Indication 883.3.6 Tetracyclines 883.3.6.1 Mechanism of Action 883.3.6.2 Clinical Indication 883.3.7 Aminoglycosides 893.3.7.1 Mechanism of Action 893.3.7.2 Clinical Indication 893.4 Antifungal Agents 893.4.1 Polyenes 903.4.1.1 Mechanism of Action 903.4.1.2 Clinical Indication 903.4.2 Azoles 903.4.2.1 Mechanism of Action 903.4.2.2 Clinical Indication 933.4.3 Echinocandins 933.4.3.1 Mechanism of Action 943.4.3.2 Clinical Indication 943.4.4 Flucytosine 953.4.4.1 Mechanism of Action 953.4.4.2 Clinical Implication 953.5 Antiviral agents 953.6 Antiparasitic Agents 983.6.1 Antiprotozoan Agents 983.6.2 Antihelminthic Agents 1013.6.3 Ectoparasiticides 1013.7 Antimicrobial Resistance 1013.7.1 Genetic Basis of AMR 1023.7.2 Mechanistic Basis of Antimicrobial Resistance 1023.8 Conclusion 103Acknowledgment 104References 1044 Trends in Antimicrobial Therapy: Current Approaches and Future Prospects 111 Mohan Kumar Verma, Santhalingam Gayathri, BalasubramaniemAshokkumar, and Perumal Varalakshmi4.1 Introduction 1114.2 Antibiotics: A Brief History 1124.2.1 Classification of Antibiotics 1134.2.2 Evolution of Antibiotics 1134.2.3 Mechanism of Action of Antibiotics 1134.3 AMR: A Global Burden 1134.3.1 Global Scenario 1144.3.2 Origin of SUPERBUGS and the “END of Antibiotics” 1164.4 Antimicrobial Resistance and Virulence 1174.4.1 Molecular Insights and Mechanism of AMR 1174.4.2 Antibiotic Resistance in Bacteria 1184.4.2.1 Horizontal Gene Transfer 1184.4.2.2 Increased Mutation Rate 1184.4.2.3 Antibiotic Inactivation 1184.4.2.4 Alteration of the Antibiotic Targets 1194.4.2.5 Changes in Cell Permeability and Efflux 1194.4.2.6 The Major Facilitator Superfamily 1194.4.2.7 The ATP-Binding Cassette Superfamily 1194.4.2.8 The Multidrug and Toxic Compound Extrusion Family 1204.4.2.9 The Resistance–Nodulation–Division (RND) Superfamily 1204.4.2.10 The Small Multidrug-Resistance Family 1204.4.3 Development of Antibiotic Resistance 1204.4.4 Prioritization of Antibiotic Resistant Bacteria 1204.4.5 Understanding Biofilm Resistance 1224.5 Alternatives to Antibiotics 1224.5.1 Peptide Antibiotics 1224.5.1.1 Cationic Antimicrobial Peptides (CAMPs) 1224.5.1.2 Marine Antimicrobial Peptides 1234.5.2 Nano Drugs 1244.5.3 Probiotics 1254.5.4 Bacteriocins 1264.5.5 Bdellovibrio 1274.5.6 Bdellovibrio as Live Antimicrobial Agent 1284.6 Antibiotics: Global Action Plan on Antimicrobial Resistance 1294.7 Conclusion 130Acknowledgment 130References 1315 Fermentation Strategies in the Food and Beverage Industry 141 Mohit Bibra, R. Navanietha Krishnaraj, and Rajesh K. Sani5.1 Introduction 1415.2 Current Trends in Food Fermentation 1435.2.1 Fermentation Types 1445.2.1.1 Spontaneous Fermentation 1445.2.1.2 Back-Slopping Fermentation 1445.2.1.3 Starter-Culture Fermentation 1445.2.2 Microbial Cultures 1455.2.2.1 Starter Cultures 1455.2.2.2 Adjunct Cultures 1555.2.2.3 Bio-protective Cultures 1555.2.2.4 Probiotic Cultures 1555.3 Future Directions 1565.3.1 Use of Defined Mixed Cultures 1565.3.2 Nanotechnology 1575.3.2.1 Nanosensors 1575.3.2.2 Nanoparticles 1575.3.2.3 Nanocomposites 1575.3.3 Meat Analogues 1585.4 Conclusions 1585.5 Questions for Thought 159References 1606 Bioactive Oligosaccharides: Production, Characterization, and Applications 165R. Aanandhalakshmi, K. Sundar, and B. Vanavil6.1 Introduction 1656.2 Sources, Types, Structure of Oligosaccharides 1666.2.1 Plant Source 1666.2.2 Animal Source 1676.2.3 Insect Source 1676.2.4 Marine Source 1676.2.5 Microbial Source 1686.2.6 Synthetic Oligosaccharides 1686.2.7 Pseudo-oligosaccharides 1686.3 Production Methods of Oligosaccharides 1696.3.1 Chemical Methods 1696.3.2 Physical Methods 1696.3.3 Enzymatic Hydrolysis 1716.3.4 Microbial Production of Oligosaccharides 1716.4 Extraction, Separation, and Purification of Oligosaccharides 1726.5 Characterization of Oligosaccharides 1746.6 Functional Properties of Oligosaccharides 1746.7 Applications of Oligosaccharides 1756.7.1 Functional Foods, Nutraceuticals, and Prebiotics 1766.7.2 Pharmaceutical and Medical Applications 1766.7.2.1 Effects on Intestinal Microflora 1766.7.2.2 Effects on Urogenital Infections 1776.7.2.3 Type II Diabetes and Obesity 1776.7.2.4 Immunomodulatory and Antitumor Activities 1786.7.2.5 Effect on Cardiovascular Risk 1786.7.2.6 Lowering of Cholesterol 1786.7.2.7 Role in Osteoporosis 1786.7.2.8 Antihypertensive Effects 1796.7.2.9 Hepatic Protection 1796.7.2.10 Antioxidant and Neuroprotective Agent 1796.7.2.11 Antimicrobial Activity 1806.7.2.12 Antibiotics 1806.7.2.13 Oligosaccharides as Vaccine Components 1816.7.3 Environmental Fortification 1816.7.4 Cosmetics 1826.7.5 Elicitors and Agriculture 1826.7.6 Novel Biomaterials 1836.8 Market Potential of Oligosaccharides 1836.9 Future Prospects 184References 1847 Biopolymers: A Retrospective Analysis in the Facet of Biomedical Engineering 201 Gayathri Ravichandran and Aravind Kumar Rengan7.1 Introduction 2017.2 Natures’ Advanced Materials: A Glance at Its Structure and Properties 2027.2.1 Polypeptides 2027.2.1.1 Collagen 2027.2.1.2 Elastin 2027.2.1.3 Silk Fibroin 2047.2.1.4 Gelatin 2047.2.1.5 Albumin 2057.2.1.6 Casein 2057.2.2 Polysaccharides 2057.2.2.1 Cellulose 2057.2.2.2 Starch 2067.2.2.3 Cyclodextrin 2077.2.2.4 Hyaluronic Acid 2077.2.2.5 Chitosan 2087.2.2.6 K-carrageenan 2087.2.2.7 Agarose 2097.2.2.8 Alginate 2097.2.3 Polynucleotides-based Biopolymers 2107.3 Smart Biopolymers 2117.3.1 Chemical-Responsive Biopolymers 2117.3.1.1 pH-Sensitive Smart Biopolymers 2117.3.1.2 Glucose-Responsive Biopolymers 2127.3.2 Physically Responsive Biopolymers 2127.3.2.1 Temperature-Sensitive Smart Biopolymers 2127.3.2.2 Light-Responsive Smart Polymers 2137.3.2.3 Electric-Responsive Smart Polymers 2137.3.2.4 Magnetic-Responsive Smart Polymers 2147.3.2.5 Redox-Responsive Biopolymer 2157.3.3 Biochemical Stimuli-Responsive Biopolymers 2157.3.3.1 Enzyme-Responsive Biopolymer 2157.4 Fundamental Applications of Biopolymers in Biomedical Engineering 2167.4.1 Biopolymers in Cancer Theranostics 2167.4.1.1 Drug Delivery 2177.4.1.2 Cancer Diagnosis and Molecular Imaging 2187.4.2 Biopolymeric-based Biosensor 2197.4.3 Wound Healing 2227.4.4 Tissue Engineering and Regenerative Medicine 2237.4.4.1 Biopolymers as Bioink for 3D Scaffolds 2257.4.4.2 Corneal Regeneration 2257.4.4.3 Neural Tissue Engineering 2267.4.4.4 Bone Tissue Engineering 2277.4.4.5 Cartilage Tissue Regeneration 2277.4.5 Biopolymers for Biological Implants 2297.4.6 Biopolymers in Other Applications 2307.5 Processing Techniques for the Contrivance of Biopolymers 2307.5.1 3D Bioprinting 2307.5.2 4D Bioprinting 2327.5.3 Electrospinning 2337.6 Conclusion 234Acknowledgments 234References 2348 Metabolic Engineering Strategies to Enhance Microbial Production of Biopolymers 247Shailendra Singh Shera and Rathindra Mohan Banik8.1 Introduction 2478.2 Microbes as Cell Factories for the Production of Speciality Biochemicals 2488.2.1 Bacteria as Cell Factories for the Production of Biopolymers 2498.2.1.1 Polysaccharides 2498.2.1.2 Polyesters 2508.2.1.3 Polyamides 2518.2.2 Fungus as Cell Factories for the Production of Biopolymers 2528.2.2.1 Polysaccharides 2538.2.2.2 Polyester 2538.2.2.3 Polyamides 2548.2.3 Microalgae as Cell Factories for the Production of Biopolymers 2548.2.3.1 Polysaccharides from Microalgae 2558.2.3.2 Polyester 2558.2.3.3 Polyamides 2568.3 Microbial Production Pathways for Various Types of Biopolymers 2568.3.1 Polysaccharide Production Pathways in Bacteria 2568.3.2 Mechanism of Fungal Polysaccharides Synthesis 2608.3.3 Mechanism of Synthesis of Polyester in Bacteria 2608.3.4 Mechanism of Synthesis of Polyamide in Bacteria 2628.4 Tools and Technologies Available for Metabolic Engineering 2628.4.1 Metabolic Pathway Reconstruction 2638.4.2 Metabolic Flux Analysis 2648.4.3 Metabolic Control Analysis 2668.4.4 Omics Analysis 2668.5 Dynamic Metabolic Flux Analysis and its Role in Metabolic Engineering 2688.6 Production of Biopolymers from Metabolically Engineered Microbes 2698.6.1 Metabolic Modification of Pathway for Synthesis of Polysaccharides 2698.6.2 Levan 2718.6.3 Metabolic Modification of Pathway for Synthesis of Polyester 2718.6.4 Metabolic Modification of Pathway for Synthesis of Polyamides 2728.6.5 Culture of Metabolically Engineered Microbes in Fermentation or Bioreactor for Production of Biopolymer 2738.7 Recovery and Purification of Biopolymers from Fermentation Broth 2758.7.1 Separation and Purification of Xanthan 2758.7.2 Separation of Poly-L- lysine 2778.8 Conclusion and Future Challenges 278Acknowledgments 278References 279Web References 2859 Bioplastics Production: What Have We Achieved? 287Tanvi Govil, David R. Salem, and Rajesh K. Sani9.1 Introduction 2879.2 Current Trends 2899.3 Different Types of Bioplastics 2919.3.1 Bio-based Polyethylene (Bio-PE) 2919.3.2 Bio-based PET 2929.3.3 Polylactic Acid 2939.3.4 Starch Blends 2949.3.5 Polyhydroxyalkanoate 2959.3.6 Polybutylene Succinate 2989.3.7 Polybutylene Adipate Terephthalate 2999.3.8 Polycaprolactone 2999.3.9 Epoxies 3009.3.10 Cellulose Acetate 3009.4 Challenges Facing the Bioplastics Industry 3019.5 Misconceptions and Negative Impacts 3019.6 Take Home Message and Future Directions 3029.7 Questions for Thought 303Acknowledgments 304Conflict of Interest 304References 30410 Conversion of Lignocellulosic Biomass to Ethanol: Recent Advances 311Ramiya Baskaran, Vignesh Natarajan, Shereena Joy, and Chandraraj Krishnan10.1 Introduction 31110.2 LCB: Structure, Composition, and Recalcitrance 31210.3 LCB to Ethanol: Bioprocess Strategies 31310.4 Pretreatment of LCB 31310.4.1 Physical Pretreatment 31610.4.2 Physicochemical Pretreatment 31910.4.2.1 Steam Explosion 32010.4.2.2 Liquid Hot Water 32010.4.2.3 Ammonia Fiber Explosion 32110.4.3 Chemical Pretreatment 32110.4.3.1 Dilute Acid Pretreatment (DAP) 32210.4.3.2 Alkali Pretreatment 32210.4.3.3 Organosolv 32310.4.3.4 Ionic Liquid (IL) and Deep Eutectic Solvent (DES) 32310.4.3.5 Supercritical Fluid Pretreatment 32410.4.4 Biological Pretreatment 32510.4.4.1 Bacterial Pretreatment 32510.4.4.2 Fungal Pretreatment 32510.4.4.3 Enzymatic Pretreatment 32610.4.5 Optimization of Pretreatment Process 32610.5 Enzymatic Hydrolysis 32710.5.1 Cellulose Hydrolysis 32710.5.2 Xylan Hydrolysis 32810.5.3 Accessory Enzymes 32810.5.4 Auxiliary Activity and Non-Hydrolytic Enzymes 33010.5.5 Enzyme Cocktail for Biomass Hydrolysis 33110.5.5.1 Cocktail Development 33110.6 High Solids Loading Enzymatic Hydrolysis (HSLEH) 33510.6.1 Enzyme Inhibitors and Detoxification 33510.6.2 Cellulase Feedback Inhibition 33610.6.3 Rheology 33710.6.4 Reactors and Impellers 33710.7 Fermentation 33810.8 Genetic Engineering in LCB Bioconversion 34310.9 Conclusions 344Acknowledgments 344References 34411 Advancement in Biogas Technology for Sustainable Energy Production 359Rouf Ahmad Dar, Saroj Bala, and Urmila Gupta Phutela11.1 Introduction 35911.2 Biogas Developments Worldwide 36011.3 Biogas Development in India 36311.4 Recent Issues in Biogas Production 36511.5 Current Trends in Biogas Production 36511.6 Advanced Anaerobic Digestion Methodologies 36711.6.1 Anaerobic Membrane Reactor (AnMBRs) 36811.6.2 Dry Anaerobic Digestion Technology (DADT) 36811.6.3 Anaerobic Co-digestion Technology (AcoD) 36911.7 Role of Biotechnology in Enhancing Biogas Production 37011.8 Application of Nanotechnology in Biogas and Methane Production 37111.9 Biogas Upgrading Technologies 37211.10 Conclusion 372References 37812 Biofertilizers: A Sustainable Approach Towards Enhancing the Agricultural Productivity 387Satya Sundar Mohanty12.1 Introduction 38712.2 Types of Biofertilizers 38812.2.1 Nitrogen-Fixing Biofertilizer 38912.2.1.1 Free-Living Nitrogen-Fixing Microorganisms 39012.2.1.2 Photosynthetic Nitrogen-Fixing Microorganisms 39012.2.2 Phosphorus Biofertilizer 39112.2.2.1 Phosphate-solubilizing Bacteria (PSB) 39212.2.2.2 Phosphate-mobilizing Microorganisms 39412.2.3 Plant-Growth- promoting Biofertilizers 39412.3 Effect on Bioremediation of Environmental Pollutants 39612.4 Bioformulations and Its Types 39812.5 Preparation of Biofertilizers 40112.6 Various Modes of Biofertilizer Application 40212.7 Challenges to Commercialization of Biofertilizers 40312.8 Future Perspective 403References 40413 Biofertilizers from Food and Agricultural By-Products and Wastes 419Veknesh Arumugam, Muhammad Heikal Ismail, and Winny Routray13.1 Introduction 41913.2 Biofertilizer 42013.2.1 N2-fixing Biofertilizer 42213.2.1.1 Free-living N2-fixing Biofertilizer 42213.2.1.2 Symbiotic N2-Fixing Biofertilizer 42413.2.2 Phosphate-solubilizing Biofertilizers 42513.2.3 Phosphate-mobilizing Biofertilizer 42513.2.4 Plant-Growth- promoting Biofertilizers 42613.3 Agricultural Waste 42613.3.1 Agro-industrial Wastes 42813.4 Food Waste 43013.5 Biofertilizer Production Using Fermentation Technology 43213.5.1 Solid-State Fermentation (SSF) 43313.5.2 Submerged Fermentation (SmF) 43513.5.3 Production of N2-fixing Biofertilizer 43813.5.3.1 Production of Rhizobium Biofertilizer 43813.5.3.2 Production of Azotobacter Biofertilizer 43813.5.3.3 Production of Azospirillum Biofertilizer 43913.5.4 Production of Phosphate-solubilizing Biofertilizer 43913.5.5 Production of Phosphate-mobilizing Biofertilizer 43913.6 Biofertilizer for Organic Farming 44013.7 Conclusion 441Conflict of Interest 441References 442Index 449