INDUSTRIAL FERMENTATIONS

By I. GIANY

Part I Enabling and Improving Large-Scale Bio-production 1 1 Industrial-Scale Fermentation 3 11 Introduction 3 12 Industrial-Scale Fermentation Today 5 121 Organisms Used in Large-Scale Fermentation 5 122 Contemporary Large-Scale Fermentation 7 123 Economic Aspects of Industrial Fermentation from a Market Perspective 14 124 The Drivers and the Future of Industrial Fermentation 15 13 Engineering and Design Aspects 18 131 Process Development – Scale-Up Starts at Laboratory Scale 18 132 Plant Design Aspects 19 1321 General Aspects of Plant Design 19 1322 Design Constraints and Guidelines 21 1323 Seed Lines 24 1324 Vessel Geometry 25 1325 Mixing and Mass Transfer 27 1326 Temperature Control and Heat Transfer 31 1327 Oxygenation 32 14 Industrial Design Examples 36 141 Cephalosporin C Production 36 142 Monoclonal Antibody Production at the 10m3 Scale 39 143 Nonsterile Fermentations 42 15 Cost Analysis for the Manufacture of Biotechnological Products 42 151 Investment 42 152 Operational Cost, Cost of Manufacturing 43 153 Return on Invested Capital 47 16 Influence of Process- and Facility-Related Aspects on Cost Structure 47 161 Process-Related Aspects 48 162 Site-Related Aspects 48 Acknowledgments 51 References 52 2 Scale-Down: Simulating Large-Scale Cultures in the Laboratory 55 21 Introduction 55 22 Heterogeneities at Large Scale and the Need for Scaling Down 56 23 Bioreactor Scale-Down 58 24 Tools to Study Cell Responses to Environmental Heterogeneities 62 241 Scale-Down Simulators 62 2411 One-Compartment Scale-Down Systems 63 2412 Multicompartment Scale-Down Systems 64 242 Analytical Techniques 66 2421 Metabolic Studies 66 2422 Differential Gene Expression and Protein Accumulation 67 2423 Physical Measurements 67 2424 Mathematical Modeling 68 25 Physiological Effects of Environmental Heterogeneities 68 251 Negative Effects 68 2511 Negative Effects on Animal Cells 70 252 Positive Effects 71 253 Further Observations 72 26 Improvements Based on Scale-Down Studies: Bioreactor Design and Cell Engineering 72 27 Perspectives 73 Acknowledgment 74 References 74 3 BioreactorModeling 81 31 Large-Scale Industrial Fermentations: Challenges for Bioreactor Modeling 81 311 Global Status 81 312 Perspectives 82 32 Bioreactors 83 321 Stirred-Tank Bioreactors 83 322 Bubble Columns and Air-Lift Reactors 86 323 Other Reactors 86 324 Bioreactor Modeling 87 33 Compartment and Hybrid Multizonal/Computational Fluid Dynamics Approaches for the Description of Large-Scale Bioreactor Phenomena 89 331 Compartment Models 89 332 Hybrid Multizonal/CFD Models 91 34 Computational Fluid Dynamics Modeling: Unstructured Continuum Approach (Euler–Euler) 92 341 Introduction 92 342 Single Phase 93 3421 Turbulence Modeling 95 343 Two-Phase Flow 100 3431 Approaches 100 3432 Euler–Euler Model 100 3433 Interaction Forces 102 3434 Turbulence Modeling 103 344 CFD of Gassed Stirred Tanks 104 3441 Bubble Size 105 3442 Glucose Uptake 110 3443 Oxygen Uptake – Distribution of Dissolved Oxygen 111 345 Summary of CFD 112 35 Computational Fluid Dynamics Modeling: Structured Segregated Approach (Euler–Lagrange) 114 351 Introduction 114 352 Euler–Lagarange Modeling 115 353 Metabolic Structuring 117 354 Model Simulations and Detailed Insight into Cell Responses to Dynamic Conditions in Large Bioreactors 118 36 Conclusion 122 37 Outlook 122 References 124 4 Cell Culture Technology 129 41 Introduction 129 42 Overview of Applications for Cell Culture Products and Tissue Engineering 129 43 Fundamentals 131 431 Cell Sources 131 432 Cell Physiology and Kinetics for Process Engineering 132 433 Population Dynamics, Cell-Cycle Dependence, and Implications on Process Control 134 4331 Separation Methods and Analytics 135 4332 Population-Resolved Modeling and Data Treatment 136 4333 Population-Resolved Online Monitoring and Process Control 138 434 Medium Design 139 44 Bioreactors for Cell Culture 140 441 Requirements 140 442 Bioreactors for Suspended Cells 142 443 Single-Use Bioreactors 144 444 Fixed-Bed and Fluidized-Bed Reactors 144 445 Hollow-Fiber and Membrane Reactors 145 446 Process Strategies and Control 145 45 Downstream 146 46 Regulatory and Safety Issues 150 47 Conclusions and Outlook 152 References 152 Part II Getting Out More: Strategies for Enhanced Bioprocessing 159 5 Production of Fuels and Chemicals from Biomass by Integrated Bioprocesses 161 51 Introduction 161 52 Utilization of Starchy Biomass 163 521 Pretreatment and Enzymatic Hydrolysis of Starch 163 522 Consolidated Bioprocessing for Starch Utilization 164 53 Utilization of Lignocellulosic Biomass 166 531 Pretreatment and Enzymatic Hydrolysis of Lignocellulose 166 532 Consolidated Bioprocessing for Lignocellulose Utilization 167 5321 Introduction 167 5322 Production of Chemicals with Native Cellulase-Producing Microbes 168 5323 Production of Chemicals with Recombinant Cellulose-Utilizing Microbes 169 54 Conclusions and Perspectives 177 Acknowledgment 177 References 178 6 Solid-State Fermentation 187 61 Introduction 187 62 Fundamentals Aspects of SSF 188 621 Selection of Microorganisms 188 622 Specific Growth Rate 189 6221 Biomass Measurement 192 63 Factors Affecting Solid-State Fermentation 193 631 Moisture 193 632 Water Activity 193 633 Temperature 194 634 pH 194 635 Inoculum Type 194 636 Substrates 194 6361 Particle Size 195 637 Aeration and Agitation 196 64 Scale-Up 196 641 Large-Scale Inoculum Development 196 642 Medium Sterilization 196 643 Aeration and Agitation 197 644 Heat Removal and Moisture Balance 197 645 pH Control 198 65 Product Recovery 198 66 Bioreactor Designing 198 661 Shallow-Tray Fermenter 199 662 Column/Fixed-Bed Fermenters 199 663 Rotating-Drum Bioreactors 199 67 Kinetics and Modeling 200 68 Applications 201 69 Challenges in SSF 202 610 Summary 203 References 203 7 Cell Immobilization: Fundamentals, Technologies, and Applications 205 71 Introduction 205 72 Fundamentals of Cell Immobilization 206 73 Immobilization with Support Materials 207 731 Surface Attachment 208 7311 Adsorption 208 7312 Covalent Binding 209 7313 Biofilm Formation 209 732 Entrapment 210 7321 Entrapment in Gel Matrixes 210 7322 Entrapment in Porous Particles 210 733 Encapsulation 211 734 Membrane Retention 212 74 Self-Immobilization 212 741 Microorganisms 213 7411 Prokaryotic Cells 213 7412 Eukaryotic Cells 214 742 Plant Cells 218 75 Immobilized Cells and their Applications 218 751 Microorganisms 219 752 Plant Cells 221 753 Mammalian and Insect cells 221 76 Bioreactors for Cell Immobilization 225 761 Stirred-Tank Bioreactor 226 762 Packed-Bed Bioreactor 227 763 Fluidized-Bed Bioreactor 227 764 Air-Lift Bioreactor 228 765 Membrane Bioreactor 228 77 Challenges and Recommendations for Future Research 229 78 Conclusions 230 References 231 Part III Molecules for Human Use: High-Value Drugs, Flavors, and Nutraceuticals 237 8 Anticancer Drugs 239 81 Natural Products as Anticancer Drugs 239 82 Anticancer Drug Production 239 821 Production Systems 239 822 Approaches for Improving Production 241 823 Gene Discovery 242 83 Important Anticancer Natural Products 243 831 Vinca Alkaloids 243 832 Taxane Diterpenoids 250 833 Podophyllotoxin Lignans 256 834 Camptothecin Quinoline Alkaloids 258 84 Prospects 261 841 Identification of Intermediates in the Biosynthetic Pathways of Anticancer Drugs 261 842 Discovery of Unknown Genes in Biosynthetic Pathways 262 843 Production of Anticancer Drugs in Microbial Hosts 262 References 263 9 Biotechnological Production of Flavors 271 91 History 271 92 Survey on Today’s Industry 272 93 Regulations 273 94 Flavor Production 274 95 Biotechnological Production of Flavors 275 951 Traditional Fermentations 275 952 De novo Synthesis 276 953 Bioconversions 277 96 Vanillin 277 961 From Eugenol 278 962 From Isoeugenol 278 963 From Ferulic Acid 280 964 From Lignin 281 97 2-Phenylethanol 281 98 Benzaldehyde 283 99 Lactones 285 910 Raspberry Ketone 289 911 Green Notes 291 912 Nootkatone 293 913 Future Perspectives 296 References 297 10 Nutraceuticals (Vitamin C, Carotenoids, Resveratrol) 309 101 Introduction 309 102 Vitamin C 310 1021 Production of L-AA by Chemical Synthesis 311 1022 Production of L-AA by a Two-Step Fermentation Process 311 1023 Classical Two-Step Fermentation Process 312 1024 New Two-Step Fermentation Process 313 1025 Production of L-AA by a One-Step Fermentation Process 314 1026 Classical Two-Step Fermentation Process-Based Attempts 314 1027 New Two-Step Fermentation Process-Based Attempts 316 1028 Reconstruction of L-AA Biosynthesis Pathway from Higher Organisms in Microorganisms 316 103 Carotenoids 317 1031 Biosynthesis of Carotenoids 319 1032 Metabolic Engineering of Carotenoid Biosynthesis in Microbes 321 104 Resveratrol 323 1041 Biosynthesis of Resveratrol and Its Derivatives 324 1042 Metabolic Engineering of Resveratrol and its Derivatives 327 105 Future Perspectives 329 References 330 Part IV Industrial Amino Acids 337 11 Glutamic Acid Fermentation: Discovery of Glutamic Acid-Producing Microorganisms, Analysis of the ProductionMechanism, Metabolic Engineering, and Industrial Production Process 339 111 Introduction 339 112 Discovery of the Glutamic Acid-Producing Bacterium Cglutamicum 340 1121 Glutamic Acid Production Prior to the Discovery of Glutamic Acid-Producing Microorganisms 340 1122 Discovery of C glutamicum, a Glutamic Acid-Producing Bacterium 340 1123 Characteristics of C glutamicum 342 113 Analysis of the Mechanism of Glutamic Acid Production by C glutamicum 342 1131 Relationship between Cell-Surface Structure and Glutamic Acid Production in C glutamicum 343 1132 Metabolic Regulation during Glutamic Acid Overproduction in C glutamicum 345 11321 Biosynthesis of Glutamic Acid in C glutamicum 345 11322 Relationship between Enzyme Activity of the 2-Oxoglutarate Dehydrogenase Complex and Glutamic Acid Production 346 11323 OdhI Decreases the Enzymatic Activity of the 2-Oxoglutarate Dehydrogenase Complex 347 11324 Anaplerotic Reactions in Glutamic Acid Overproduction 348 1133 Involvement of a Mechanosensitive Channel, NCgl1221, in Glutamic Acid Secretion in C glutamicum 349 114 Metabolic Engineering of C glutamicum for Glutamic Acid Production 350 1141 Metabolic Engineering 350 1142 Metabolic Flux Analysis in Glutamic Acid Production 350 11421 Analysis of the Impact of Activities of Enzymes Related to Glutamic Acid Production on the Flux of Glutamic Acid Production 351 11422 Use of 13C-MFA to Investigate the Importance of Anaplerotic Reactions to Glutamic Acid Production 351 1143 Metabolic Engineering for Improvement of Glutamic Acid Production 351 115 Glutamic Acid Fermentation by Other Microorganisms 352 116 Industrial Process of Glutamic Acid Production 353 117 Future Perspectives 354 References 355 12 L-Lysine 361 121 Uses of L-Lysine 361 1211 Feed Use of Amino Acids 361 1212 Economic Importance and Means of Production of L-Lysine 362 122 Biosynthesis and Production of L-Lysine 363 1221 L-Lysine Biosynthesis 363 1222 Strain Development for the Production of L-Lysine 363 12221 L-Lysine Transport 365 12222 De-bottlenecking L-Lysine Biosynthesis 366 12223 NADPH Supply for L-Lysine Production 366 12224 Reduction of Byproducts of L-Lysine Production 367 12225 Precursor Supply for L-Lysine Production 367 1223 Industrial Processes of L-Lysine Production 368 1224 Flexible Feedstock Concept of C glutamicum: Engineering Carbon Source Utilization 369 12241 Molasses, Glucose, Fructose, Sucrose, and Starch 370 12242 Lignocellulosics, Cellulose, Xylose, Arabinose, Acetate, Galactose 371 12243 Silage Juice and Lactic Acid 373 12244 Amino Sugars 373 12245 Dicarboxylic Acids 374 12246 Glycerol 374 123 The Chassis Concept: Biotin Prototrophy and Genome Reduction 374 1231 Engineering Biotin Prototrophic C glutamicum 375 1232 Genome-Streamlined C glutamicum Strains 375 124 L-Lysine Biosensors for Strain Selection and on-Demand Flux Control 377 1241 Transcriptional Regulators as Diagnostic Metabolite Sensors for Screening 377 1242 Riboswitches as Metabolite Sensors for on-Demand Metabolic Flux Control 379 125 Perspective 380 References 380 Part V Bio-Based Monomers and Polymers 391 13 Diamines for Bio-Based Materials 393 131 Introduction 393 132 DiamineMetabolism in Bacteria 395 133 Putrescine – 1,4-Diaminobutane 395 1331 Metabolism of Putrescine 396 1332 Biosynthesis and Pathway Regulation 396 1333 Metabolic Engineering for Putrescine Production 398 134 Cadaverine – 1,5-Diaminopentane 399 1341 Metabolism of Diaminopentane 399 1342 Biosynthesis and Pathway Regulation 400 1343 Metabolic Engineering for Cadaverine Production 400 1344 Bio-Based Polyamide PA510 – A Success Story 403 135 Conclusions and Perspectives 403 References 404 14 Microbial Production of 3-Hydroxypropionic Acid 411 141 Introduction 411 142 3-HP Obtained from Native Producers 413 1421 3-HP as an Intermediate of CO2 Fixation 413 1422 Degradation Pathways 415 14221 Acrylic Acid 415 14222 Pyrimidines (Uracil andThymine) 415 1423 3-HP as a Nematicide 417 143 Synthesis of 3-HP from Glucose 417 144 Synthesis of 3-HP from Glycerol 421 1441 CoA-Independent dha Operon 422 1442 CoA-Dependent pdu Operon 425 1443 Redirecting the Flux toward 3-HP Production 426 1444 K pneumoniae as a Host for Glycerol-Derived 3-HP Production 426 1445 3-HP Production from Glycerol in Recombinant E coli 431 145 Bridging the Gap Between Glucose and Glycerol in 3-HP Production 437 146 Other Strains for 3-HP Production from Glycerol 438 147 Limitations of 3-HP Synthesis 440 148 Conclusions and Future Prospects 442 Acknowledgments 443 References 444 15 Itaconic Acid – An Emerging Building Block 453 151 Background, History, and Economy 453 152 Biosynthesis of Itaconic Acid 455 1521 Aspergillus terreus 455 1522 Genes and Enzymes Involved in the Biosynthesis of Itaconic Acid in A terreus 455 1523 Genes and Enzymes Involved in the Biosynthesis of Itaconic Acid in Ustilago maydis 459 153 Production Conditions for Itaconic Acid 459 154 Physiological Effects and Metabolism of Itaconic acid 461 155 Metabolic Engineering for Itaconic Acid Production 462 156 Outlook 467 Acknowledgments 468 References 469 Part VI Top-Value Platform Chemicals 473 16 Microbial Production of Isoprene: Opportunities and Challenges 475 161 Introduction 475 162 The Milestones of Isoprene Production 476 163 Microbial Production of Isoprene: Out of the Laboratory 477 1631 Advantages of Bioisoprene Against Petroleum-Derived Isoprene 477 1632 Metabolic Pathways and Key Enzyme of Bioisoprene 477 1633 Metabolic Engineering of MVA and MEP Pathways for Microbial Production of Isoprene 480 1634 Substrate for the Microbial Production of Isoprene 481 1635 Evaluation of Isoprene Biosynthetic Process from Different Substrates 482 1636 Chassis Strains for the Microbial Production of Isoprene 485 1637 Recovery Techniques for the Gas-Phase Bioisoprene 486 1638 Scale-up Fermentation and Process Control of Bioisoprene 487 164 Main Challenges for Bioisoprene Production 489 165 Future Prospects 491 1651 Rational Design of Central Metabolic Pathway to Increase the Yield and Productivity of Isoprene 491 1652 Improving the Yield via Metabolic Pathways (MVA/MEP) Engineering 492 1653 Improving the Intermediate Precursors via Enzyme Engineering 494 1654 Novel Substrates for Bioisoprene 494 1655 Integration of Bio and Chemo Substrates and Process for Isoprene Production 495 1656 Novel Hosts for Isoprene Production 495 1657 Exploring Anaerobic Routes 496 1658 Biosynthesis of Value-Added Isoprene Derivatives 497 Acknowledgments 498 References 498 17 Succinic Acid 505 171 Introduction 505 172 Development of Succinic Acid Producers and Fermentation Strategies 506 1721 Actinobacillus succinogenes 507 1722 Anaerobiospirillum succiniciproducens 510 1723 Corynebacterium glutamicum 512 1724 Escherichia coli 515 1725 Mannheimia succiniciproducens 526 1726 Saccharomyces cerevisiae 530 173 Succinic Acid Recovery and Purification 533 1731 Precipitation 533 1732 Electrodialysis 534 1733 Reactive Extraction 535 1734 Adsorption 536 174 Summary 536 Acknowledgments 537 References 537 Part VII Biorenewable Fuels 545 18 Ethanol: A Model Biorenewable Fuel 547 181 Introduction 547 182 Metabolic Engineering: Design, Build, Test, Learn 549 1821 Design: Metabolic Pathway Engineering 550 18211 Introduction of a Foreign Pathway to Enable Non-native Substrate Utilization 550 18212 Introduction of a Foreign Pathway to Enable Homoethanol Production 552 18213 Selection of Metabolic Pathways for Modification 554 18214 Metabolic Engineering to Enable Mixed-Substrate Utilization 554 18215 Selection of Pathway Components for Tuning 555 1822 Design: Membrane Engineering for Improved Tolerance 555 1823 Build: Targeted Genetic Manipulation Techniques 556 18231 One-Step Chromosomal Editing of E coli 556 18232 Shuttle Vectors for S cerevisiae Engineering 556 18233 CRISPR/Cas 9 557 1824 Build: Evolutionary Strain Improvement 557 18241 Genome-Wide Evolution for Improved Tolerance and Production 557 18242 Enzyme Evolution to Enable Nonrecombinant Homoethanol Production 558 1825 Test: Screening of Expression Libraries 559 18251 Expression Libraries Containing Sequence Variants of a Preselected Gene 559 18252 Expression Libraries that Alter Gene Abundance 560 18253 Expression Libraries that Vary Genomic Integration Site 560 1826 Learn: Identifying Strategies and Targets for the Next Design Stage 561 18261 Reverse Engineering of Improved Strains 561 18262 Learn: Identification of Metabolic Burdens During Production 562 183 Biomass Deconstruction 563 184 Closing Remarks 564 Acknowledgments 564 References 564 19 Microbial Production of Butanols 573 191 Introduction 573 192 A Historical Perspective of n-Butanol Production 574 193 ABE Fermentation 575 1931 The Biochemistry of ABE Fermentation 575 1932 Developing Genetics Tools in Clostridium acetobutylicum 577 1933 Metabolic Engineering of Clostridium acetobutylicum for Butanol Fermentation 578 194 n-Butanol Production in Non-native Producers 580 1941 Rationale for Using Non-native Producers 580 1942 Pathways for n-Butanol Biosynthesis 580 1943 Improved n-Butanol Production with Driving Forces 582 195 Isobutanol Production 583 1951 The Biochemistry of Isobutanol Production 583 1952 Isobutanol Production from Sugar 584 1953 Isobutanol Production from Cellulose 586 1954 Isobutanol Production from CO2 586 1955 Isobutanol Production fromWaste Protein 587 1956 Isobutanol Tolerance of E coli 588 1957 Other Products from the Keto-Acid Pathway 588 196 Summary and Outlook 589 Acknowledgments 589 References 589