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Cyanobacteria Biotechnology. Edition No. 1. Advanced Biotechnology

  • ID: 5185956
  • Book
  • May 2021
  • 560 Pages
  • John Wiley and Sons Ltd

Unites a biological and a biotechnological perspective on cyanobacteria, and includes the industrial aspects and applications of cyanobacteria

Cyanobacteria Biotechnology offers a guide to the interesting and useful features of cyanobacteria metabolism that keeps true to a biotechnology vision. In one volume the book brings together both biology and biotechnology to illuminate the core acpects and principles of cyanobacteria metabolism.

Designed to offer a practical approach to the metabolic engineering of cyanobacteria, the book contains relevant examples of how this metabolic "module" is currently being engineered and how it could be engineered in the future. The author includes information on the requirements and real-world experiences of the industrial applications of cyanobacteria. This important book:

  • Brings together biology and biotechnology in order to gain insight into the industrial relevant topic of cyanobacteria
  • Introduces the key aspects of the metabolism of cyanobacteria
  • Presents a grounded, practical approach to the metabolic engineering of cyanobacteria
  • Offers an analysis of the requirements and experiences for industrial cyanobacteria
  • Provides a framework for readers to design their own processes

Written for biotechnologists, microbiologists, biologists, biochemists, Cyanobacteria Biotechnology provides a systematic and clear volume that brings together the biological and biotechnological perspective on cyanobacteria.

Note: Product cover images may vary from those shown

Foreword: Cyanobacteria Biotechnology xv

Acknowledgments xviii

Part I Core Cyanobacteria Processes 1

1 Inorganic Carbon Assimilation in Cyanobacteria: Mechanisms, Regulation, and Engineering 3
Martin Hagemann, Shanshan Song, and Eva-Maria Brouwer

1.1 Introduction – The Need for a Carbon-Concentrating Mechanism 3

1.2 The Carbon-Concentrating Mechanism (CCM) Among Cyanobacteria 4

1.2.1 Ci Uptake Proteins/Mechanisms 5

1.2.2 Carboxysome and RubisCO 8

1.3 Regulation of Ci Assimilation 10

1.3.1 Regulation of the CCM 10

1.3.2 Further Regulation of Carbon Assimilation 13

1.3.3 Metabolic Changes and Regulation During Ci Acclimation 14

1.3.4 Redox Regulation of Ci Assimilation 15

1.4 Engineering the Cyanobacterial CCM 16

1.5 Photorespiration 17

1.5.1 Cyanobacterial Photorespiration 17

1.5.2 Attempts to Engineer Photorespiration 19

1.6 Concluding Remarks 20

Acknowledgments 21

References 21

2 Electron Transport in Cyanobacteria and Its Potential in Bioproduction 33
David J. Lea-Smith and Guy T. Hanke

2.1 Introduction 33

2.2 Electron Transport in a Bioenergetic Membrane 34

2.2.1 Linear Electron Transport 34

2.2.2 Cyclic Electron Transport 37

2.2.3 ATP Production from Linear and Cyclic Electron Transport 37

2.3 Respiratory Electron Transport 38

2.4 Role of Electron Sinks in Photoprotection 41

2.4.1 Terminal Oxidases 41

2.4.2 Hydrogenase and Flavodiiron Complexes 41

2.4.3 Carbon Fixation and Photorespiration 43

2.4.4 Extracellular Electron Export 44

2.5 Regulating Electron Flux into Different Pathways 45

2.5.1 Electron Flux Through the Plastoquinone Pool 45

2.5.2 Electron Flux Through Fdx 46

2.6 Spatial Organization of Electron Transport Complexes 47

2.7 Manipulating Electron Transport for Synthetic Biology Applications 48

2.7.1 Improving Growth of Cyanobacteria 49

2.7.2 Production of Electrical Power in BPVs 49

2.7.3 Hydrogen Production 50

2.7.4 Production of Industrial Compounds 50

2.8 Future Challenges in Cyanobacterial Electron Transport 51

References 52

3 Optimizing the Spectral Fit Between Cyanobacteria and Solar Radiation in the Light of Sustainability Applications 65
Klaas J. Hellingwerf, Que Chen, and Filipe Branco dos Santos

3.1 Introduction 65

3.2 Molecular Basis and Efficiency of Oxygenic Photosynthesis 67

3.3 Fit Between the Spectrum of Solar Radiation and the Action Spectrum of Photosynthesis 72

3.4 Expansion of the PAR Region of Oxygenic Photosynthesis 74

3.5 Modulation and Optimization of the Transparency of Photobioreactors 79

3.6 Full Control of the Light Regime: LEDs Inside the PBR 81

3.7 Conclusions and Prospects 82

References 83

Part II Concepts in Metabolic Engineering 89

4 What We Can Learn from Measuring Metabolic Fluxes in Cyanobacteria 91
Xiang Gao, Chao Wu, Michael Cantrell, Melissa Cano, Jianping Yu, and Wei Xiong

4.1 Central Carbon Metabolism in Cyanobacteria: An Overview and Renewed Pathway Knowledge 91

4.1.1 Glycolytic Routes Interwoven with the Calvin Cycle 91

4.1.2 Tricarboxylic Acid Cycling 94

4.2 Methodologies for Predicting and Quantifying Metabolic Fluxes in Cyanobacteria 95

4.2.1 Flux Balance Analysis and Genome-Scale Reconstruction of Metabolic Network 95

4.2.2 13C-Metabolic Flux Analysis 96

4.2.3 Thermodynamic Analysis and Kinetics Analysis 99

4.3 Cyanobacteria Fluxome in Response to Altered Nutrient Modes and Environmental Conditions 101

4.3.1 Autotrophic Fluxome 101

4.3.2 Photomixotrophic Fluxome 104

4.3.3 Heterotrophic Fluxome 105

4.3.4 Photoheterotrophic Fluxome 105

4.3.5 Diurnal Metabolite Oscillations 106

4.3.6 Nutrient States’ Impact on Metabolic Flux 107

4.4 Metabolic Fluxes Redirected in Cyanobacteria for Biomanufacturing Purposes 108

4.4.1 Restructuring the TCA Cycle for Ethylene Production 108

4.4.2 Maximizing Flux in the Isoprenoid Pathway 109

4.4.2.1 Measuring Precursor Pool Size to Evaluate Potential Driving Forces for Isoprenoid Production 109

4.4.2.2 Balancing Intermediates for Increased Pathway Activity 110

4.4.2.3 Kinetic Flux Profiling to Detect Bottlenecks in the Pathway 111

4.5 Synopsis and Future Directions 112

Acknowledgments 112

References 112

5 Synthetic Biology in Cyanobacteria and Applications for Biotechnology 123
Elton P. Hudson

5.1 Introduction 123

5.2 Getting Genes into Cyanobacteria 123

5.2.1 Transformation 123

5.2.2 Expression from Episomal Plasmids 125

5.2.3 Delivery of Genes to the Chromosome 127

5.3 Basic Synthetic Control of Gene Expression in Cyanobacteria 129

5.3.1 Quantifying Transcription and Translation in Cyanobacteria 130

5.3.2 Controlling Transcription with Synthetic Promoters 134

5.3.2.1 Constitutive Promoters 136

5.3.2.2 Regulated Promoters that Are Sensitive to Added Compounds (Inducible) 137

5.3.2.3 CRISPR Interference for Transcriptional Repression 139

5.3.3 Controlling Translation 141

5.3.3.1 Ribosome Binding Sites (Cis-Acting) 141

5.3.3.2 Riboswitches (Cis-Acting) 142

5.3.3.3 Small RNAs (Trans-Acting) 143

5.4 Exotic Signals for Controlling Expression 143

5.4.1 Oxygen 144

5.4.2 Light Color 144

5.4.3 Cell Density or Growth Phase 145

5.4.4 Engineering Regulators for Altered Sensing Properties: State of the Art 147

5.5 Advanced Regulation: The Near Future 148

5.5.1 Logic Gates and Timing Circuits 148

5.5.2 Orthogonal Transcription Systems 151

5.5.3 Synthetic Biology Solutions to Increase Stability 152

5.5.4 Synthetic Biology Solutions for Cell Separation and Product Recovery 154

5.6 Conclusions 157

Acknowledgments 158

References 158

6 Sink Engineering in Photosynthetic Microbes 171
María Santos-Merino, Amit K. Singh, and Daniel C. Ducat

6.1 Introduction 171

6.2 Source and Sink 172

6.3 Regulation of Sink Energy in Plants 177

6.3.1 Sucrose and Other Signaling Carbohydrates 178

6.3.2 Hexokinases 179

6.3.3 Sucrose Non-fermenting Related Kinases 180

6.3.4 TOR Kinase 181

6.3.5 Engineered Pathways as Sinks in Photosynthetic Microbes 182

6.3.6 Sucrose 183

6.3.7 2,3-Butanediol 187

6.3.8 Ethylene 187

6.3.9 Glycerol 188

6.3.10 Isobutanol 188

6.3.11 Isoprene 189

6.3.12 Limonene 189

6.3.13 P450, an Electron Sink 190

6.4 What Are Key Source/Sink Regulatory Hubs in Photosynthetic Microbes? 191

6.5 Concluding Remarks 194

Acknowledgment 195

References 195

7 Design Principles for Engineering Metabolic Pathways in Cyanobacteria 211
Jason T. Ku and Ethan I. Lan

7.1 Introduction 211

7.2 Cofactor Optimization 212

7.2.1 Recruiting NADPH-Dependent Enzymes Wherever Possible 215

7.2.2 Engineering NADH-Specific Enzymes to Utilize NADPH 217

7.2.3 Increasing NADH Pool in Cyanobacteria Through Expression of Transhydrogenase 218

7.3 Incorporation of Thermodynamic Driving Force into Metabolic Pathway Design 219

7.3.1 ATP Driving Force in Metabolic Pathways 220

7.3.2 Increasing Substrate Pool Supports the Carbon Flux Toward Products 222

7.3.3 Product Removal Unblocks the Limitations of Product Titer 223

7.4 Development of Synthetic Pathways for Carbon Conserving Photorespiration and Enhanced Carbon Fixation 225

7.5 Summary and Future Perspective on Cyanobacterial Metabolic Engineering 229

References 229

8 Engineering Cyanobacteria for Efficient Photosynthetic Production: Ethanol Case Study 237
Guodong Luan and Xuefeng Lu

8.1 Introduction 237

8.2 Pathway for Ethanol Synthesis in Cyanobacteria 238

8.2.1 Pyruvate Decarboxylase and Type II Alcohol Dehydrogenase 238

8.2.2 Selection of Better Enzymes in the Pdc–AdhII Pathway 240

8.2.3 Systematic Characterization of the PdcZM–Slr1192 Pathway 241

8.3 Selection of Optimal Cyanobacteria “Chassis,” Strain for Ethanol Production 242

8.3.1 Synechococcus PCC 6803 and Synechococcus PCC 7942 243

8.3.2 Synechococcus PCC 7002 245

8.3.3 Anabaena PCC 7120 245

8.3.4 Nonconventional Cyanobacteria Species 246

8.4 Metabolic Engineering Strategies Toward More Efficient and Stable Ethanol Production 246

8.4.1 Enhancing the Carbon Flux via Overexpression of Calvin Cycle Enzymes 248

8.4.2 Blocking Pathways that Are Competitive to Ethanol 248

8.4.3 Arresting Biomass Formation 249

8.4.4 Engineering Cofactor Supply 249

8.4.5 Engineering Strategies Guided by In Silico Simulation 250

8.4.6 Stabilizing Ethanol Synthesis Capacity in Cyanobacterial Cell Factories 251

8.5 Exploring the Response in Cyanobacteria to Ethanol 253

8.5.1 Response of Cyanobacterial Cells Toward Exogenous Added Ethanol 254

8.5.2 Response of Cyanobacteria to Endogenous Synthesized Ethanol 255

8.6 Metabolic Engineering Strategies to Facilitate Robust Cultivation Against Biocontaminants 256

8.6.1 Engineering Cyanobacteria Cell Factories to Adapt for Selective Environmental Stresses 256

8.6.2 Engineering Cyanobacteria Cell Factories to Utilize Uncommon Nutrients 258

8.7 Conclusions and Perspectives 258

References 259

9 Engineering Cyanobacteria as Host Organisms for Production of Terpenes and Terpenoids 267
João S. Rodrigues and Pia Lindberg

9.1 Terpenoids and Industrial Applications 267

9.2 Terpenoid Biosynthesis in Cyanobacteria 270

9.2.1 Methylerythritol-4-Phosphate Pathway 270

9.2.2 Formation of Terpene Backbones 272

9.3 Natural Occurrence and Physiological Roles of Terpenes and Terpenoids in Cyanobacteria 274

9.4 Engineering Cyanobacteria for Terpenoid Production 275

9.4.1 Metabolic Engineering 277

9.4.1.1 Terpene Synthases 277

9.4.1.2 Increasing Supply of Terpene Backbones 285

9.4.1.3 Engineering the Native MEP Pathway 286

9.4.1.4 Implementing the MVA Pathway 287

9.4.1.5 Enhancing Precursor Supply 288

9.4.2 Optimizing Growth Conditions for Production 289

9.4.3 Product Capture and Harvesting 291

9.5 Summary and Outlook 292

Acknowledgments 293

References 293

10 Cyanobacterial Biopolymers 301
Moritz Koch and Karl Forchhammer

10.1 Polyhydroxybutryate 301

10.1.1 Introduction 301

10.1.2 PHB Metabolism in Cyanobacteria 302

10.1.3 Industrial Applications of PHB 305

10.1.3.1 Physical Properties of PHB and Its Derivatives 305

10.1.3.2 Biodegradability 306

10.1.3.3 Application of PHB as a Plastic 306

10.1.3.4 Reactor Types 306

10.1.3.5 Production Process 307

10.1.3.6 Downstream Processing 308

10.1.4 Metabolic Engineering of PHB Biosynthesis 308

10.1.5 Limitations and Potential of PHB Production in Cyanobacteria 310

10.2 Cyanophycin Granules in Cyanobacteria 311

10.2.1 Biology of Cyanophycin 311

10.2.2 Genes and Enzymes of CGP Metabolism 315

10.2.2.1 Cyanophycin Synthetase 315

10.2.2.2 Cyanophycin Degrading Enzymes 316

10.2.3 Regulation of Cyanophycin Metabolism 317

10.2.4 Cyanophycin Overproduction and Potential Industrial Applications 318

Acknowledgement 319

References 319

11 Biosynthesis of Fatty Acid Derivatives by Cyanobacteria: From Basics to Biofuel Production 331
Akihito Kawahara and Yukako Hihara

11.1 Introduction 331

11.2 Overview of Fatty Acid Metabolism 332

11.2.1 Fatty Acid Biosynthesis 332

11.2.2 Fatty Acid Degradation and Turnover 335

11.2.3 Accumulation of Storage Lipids 336

11.3 Basic Technologies for Production of Free Fatty Acids 337

11.3.1 Production of Free Fatty Acids in E. coli 337

11.3.2 Production of Free Fatty Acids in Cyanobacteria 338

11.4 Advanced Technologies for Enhancement of Free Fatty Acid Production 339

11.4.1 Enhancement of Fatty Acid Biosynthesis 339

11.4.2 Enhancement of Carbon Fixation Activity 345

11.4.3 Engineering of Carbon Flow: Modification of Key Regulatory Factors 345

11.4.4 Engineering of Carbon Flow: Deletion of Competitive Pathways 346

11.4.5 Mitigation of the Toxicity of FFAs 347

11.4.6 Enhancement of FFA Secretion 348

11.4.7 Induction of Cell Lysis 349

11.4.8 Recovery of Produced FFAs from Medium 350

11.4.9 Identification of Cyanobacterial Strains Suitable for FFA Production 350

11.5 Hydrocarbon Production in Cyanobacteria 351

11.6 Advanced Technologies for Enhancement of Hydrocarbon Production 353

11.6.1 Enhancement of Alk(a/e)ne Biosynthesis 353

11.6.2 Improvement of the Performance of Alkane Biosynthetic Enzymes 354

11.7 Basic Technologies for Production of Fatty Alcohols 355

11.8 Advanced Technologies for Enhancement of Fatty Alcohol Production 355

11.9 Basic Technologies for Production of Fatty Acid Alkyl Esters 356

11.10 Perspectives 357

References 358

12 Product Export in Cyanobacteria 369
Cátia F. Gonçalves, Steeve Lima, and Paulo Oliveira

12.1 Introduction 369

12.2 Secretion Mediated by Membrane-Embedded Systems 373

12.2.1 Proteins 373

12.2.2 Extracellular Polymeric Substances (EPS) 377

12.2.3 Soluble Sugars and Organic Acids 379

12.2.4 Fatty Acids 381

12.2.5 Alcohols 382

12.2.6 Terpenes 384

12.3 MV-Mediated Secretion 386

12.3.1 Structure and Biogenesis of Bacterial MVs 386

12.3.1.1 Cyanobacterial MVs 388

12.3.2 MVs as Novel Biotechnological Tools 389

12.4 Concluding Remarks 391

Acknowledgments 392

References 392

Part III Frontiers of Cyanobacteria Biotechnology 407

13 Harnessing Solar-Powered Oxic N2-fixing Cyanobacteria for the BioNitrogen Economy 409
James Young, Liping Gu, William Gibbons, and Ruanbao Zhou

13.1 Introduction 409

13.2 Physiology and Implications of Oxic Nitrogen Fixation 410

13.2.1 Ecological Range 411

13.2.2 Balancing Photosynthesis and Nitrogen Fixation 412

13.2.3 Energetic Demands and How the Cells Adapt 412

13.2.4 Impacts of Continuous Light vs Dark–Light Cycles 416

13.3 Major Biotechnology Applications for Diazotrophic Cyanobacteria 417

13.3.1 General Economic and Environmental Considerations of Diazotrophic Cyanobacteria 417

13.3.2 Metabolic Engineering of N2-Fixing Cyanobacteria for Carbon Compound Production 420

13.3.2.1 Direct Production of Biofuels 420

13.3.2.2 Cyanobacteria as a Fermentable Substrate 420

13.3.3 Metabolic Engineering of Nitrogen Fixing Cyanobacteria for Nitrogen-Rich Compound Production 422

13.3.3.1 Ammonia 422

13.3.3.2 Guanidine 423

13.3.3.3 Cyanophycin 423

13.3.3.4 Amino Acids and Proteins 423

13.3.4 Application of Diazotrophic Cyanobacteria in Agriculture 425

13.4 Conclusions 428

References 428

14 Traits of Fast-Growing Cyanobacteria 441
Meghna Srivastava, Elton P. Hudson, and Pramod P. Wangikar

14.1 Introduction 441

14.2 Why is Growth Rate Significant? 442

14.3 An Overview of Factors Affecting the Growth Rates of Cyanobacteria 446

14.3.1 Light Intensity and Quality 448

14.3.2 Mixotrophic Growth 451

14.3.3 Circadian Rhythm 451

14.3.4 Additional Factors Relating to Growth Rates in Cyanobacteria 452

14.3.4.1 Cell Morphology 453

14.3.4.2 Genome Size 453

14.3.4.3 Saltwater Tolerance 454

14.3.4.4 Nutrient Supplementation 454

14.3.5 Carbon Storage 455

14.4 Overview of the Fast-Growing Model Cyanobacteria 455

14.4.1 Synechococcus elongatus UTEX 2973 455

14.4.2 Synechococcus elongatus PCC 11801 456

14.4.3 Synechococcus sp. PCC 11901 456

14.4.4 Synechococcus sp. PCC 7002 457

14.5 Relationship Between Light Usage and Growth Rate in Model Strains 458

14.5.1 Case Study: The pmgA Mutant of Synechocystis 458

14.5.2 Case Study: The S. elongatus 7942 and S. elongatus 2973 Strains 460

14.6 Molecular Determinants of Fast Growth of S. elongatus UTEX 2973 460

14.7 Carbon Fluxes in Fast-Growing Strains Determined Using Metabolic Flux Analysis 463

14.8 Engineering Cyanobacteria for Fast Growth 465

14.8.1 Calvin Cycle Enzymes 465

14.8.2 PEP Carboxylase 466

14.8.3 Carbon and Light Uptake Proteins 467

14.9 Conclusion 468

References 468

15 Cyanobacterial Biofilms in Natural and Synthetic Environments 477
Christian David, Rohan Karande, and Katja Bühler

15.1 Motivation 477

15.2 Introduction to Biofilms: Biology and Applications 478

15.3 Cyanobacteria in Natural Biofilms and Microbial Mats 483

15.4 Introduction to (Photo-)biotechnology 484

15.5 Benefits of Microscale Systems for (Photo-)biofilm Cultivation 487

15.6 Oxygen Accumulation and Its Impacts 488

15.7 Resource Management in Biofilms 491

15.8 Applications of Photosynthetic Biofilms 493

15.8.1 Biofilms Enable High Cell Densities 497

15.8.2 Biofilms Enable Continuous Production 498

15.9 Outlook 499

References 499

16 Growth of Photosynthetic Microorganisms in Different Photobioreactors Operated Outdoors 505
Eleftherios Touloupakis and Pietro Carlozzi

16.1 Background 505

16.1.1 Photobiological Hydrogen Production 506

16.1.2 Polyhydroxyalkanoate Production by Photosynthetic Microbes 508

16.1.3 Photobioreactors 509

16.2 Case Studies of Outdoor Cultivations of Photosynthetic Microorganisms 513

16.2.1 Outdoor Cultures of Purple Non-Sulfur Bacteria for H2 and PHB Production 513

16.2.2 Outdoor Cultures of Cyanobacteria 516

16.3 Conclusion 517

Acknowledgments 519

References 519

Index 531

Note: Product cover images may vary from those shown
Paul Hudson
Note: Product cover images may vary from those shown