Synthetic Biology

Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems.

Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems.

• Includes contributions from  leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms
• Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes
• Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications
• Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development. 

Geneticists, molecular biologists, physicists, chemists, and bioengineers

Contributors

Introduction

Synthetic Biology: What is in a Name?

Synthetic Biology: What’s New?

Synthetic Biology: What’s Next?

Section I: Synthesis and Engineering Tools in Synthetic Biology

Chapter 1. New Tools for Cost-Effective DNA Synthesis

Introduction

Oligonucleotide Synthesis

Gene Assembly

Quality Control

Applications of DNA Synthesis

Conclusion

Acknowledgments

References

Chapter 2. Protein Engineering as an Enabling Tool for Synthetic Biology

Introduction

Protein Engineering Methods

Applications of Protein Engineering in Synthetic Biology

Conclusions

References

Chapter 3. Pathway Engineering as an Enabling Synthetic Biology Tool

Introduction

Design and Construction of Pathways

Pathway Optimization

Applications of Pathway Engineering Tools

Conclusions and Future Prospects

Acknowledgments

References

Chapter 4. From Biological Parts to Circuit Design

Introduction

The Parts

Assembling Parts

Circuit Design

Conclusion

Acknowledgments

References

Section II: Computational and Theoretical Tools in Synthetic Biology

Chapter 5. Theoretical Considerations for Reprogramming Multicellular Systems

Introduction

Conceptual Framework: Gene Regulatory Networks, Network States, and Cell Types

The Quasi-Potential Landscape

How to Obtain a Trajectory on the Quasi-Potential Landscape for Transition Between Two Attractors

Example: State Transition in Blood Cell and Pancreas Cell Differentiation and Reprogramming

Conclusion and Outlook

References

Chapter 6. Computational Protein Design for Synthetic Biology

Introduction

Methods Overview

Computational Design of Protein–protein Interactions

Computational Design of Catalytic Activity

Protein Thermostabilization by Computational Design

Computational Design of (Novel) Protein Folds

Complementarity with Directed Evolution

Conclusion and Outlook

References

Chapter 7. Computer-Aided Design of Synthetic Biological Constructs with the Synthetic Biology Software Suite

Introduction

Synthetic Logical-AND Gates and Protein Devices

The Synthetic Biology Software Suite

Conclusion

Acknowledgments

References

Chapter 8. Computational Methods for Strain Design

Introduction

Fundamental Components of Synthetic Biology

Computational Prediction Tools for Synthetic Biology Components

Computational Tools for Pathway Prediction

Computational Tools for Strain Optimization

Synthetic Biology for Systems-Level Metabolic Engineering

Concluding Remarks

Acknowledgments

References

Section III: Applications in Synthetic Biology

Chapter 9. Design and Application of Synthetic Biology Devices for Therapy

Introduction

Target Organisms and Cell Types for Therapeutic Applications of Synthetic Biology

Molecular Toolkit for Synthetic Biology

Therapeutic Applications of Synthetic Biology

Conclusion: Challenges and Safety Issues

References

Chapter 10. Drug Discovery and Development via Synthetic Biology

Introduction

Tools for Pathway Discovery and Engineering

Applications

Conclusions and Future Perspectives

Acknowledgments

References

Chapter 11. Synthetic Biology of Microbial Biofuel Production: From Enzymes to Pathways to Organisms

Introduction

Pathway Design and Optimization

Host Engineering

Future Prospects

References

Chapter 12. Tools for Genome Synthesis

Introduction

DNA Size Limit by E. coli Plasmid

Genome Cloning Using a Bottom-Up Approach

The KEIO Method

Mitochondria and Chloroplast: Organelle Guest Genomes in BGM

Bottom-Up Approaches for De Novo Genome Production

Costs to Synthesize Genomes

Relevant Methods to Support Genome Synthesis

Future Perspectives of BGM Systems Accrued from the Present Achievements

Summary

References

Chapter 13. Synthetic Microbial Consortia and their Applications

Introduction

Communication in Synthetic Multicellular Systems

Engineering Unidirectional Communication

Engineered Cooperation in Synthetic Microbial Consortia

Programming Antagonistic Interactions between Populations

Spatial Organization in Synthetic Consortia

Synthetic Biofilms Lead to Stable Consortia Behavior Over a Long Period of Time

Advances in Technology Allow the Precise Spatial Arrangement of Synthetic Consortia

The Evolution of Cooperation Can Yield Novel Behaviors in Synthetic Consortia

Applications of Synthetic Consortia in Industrial Processes and Medicine

Future Challenges

References

Section IV: Future Prospects

Chapter 14. Semi-Synthetic Minimal Cells: Biochemical, Physical, and Technological Aspects

Introduction

The Conceptual Framework of Semisynthetic Minimal Cells

Reconstruction of Genetic/Metabolic Processes in Semisynthetic Minimal Cells

Physical Aspects of SSMC Construction: Implications for the Origin of Life

SSMCs as a Biotechnological Tool

Some Open Questions and Future Perspectives

Concluding Remarks

Acknowledgments

References

Chapter 15. Transforming Synthetic Biology with Cell-Free Systems

Introduction

Cell-Free Biology

Advantages of Cell-Free Biology

Existing Technologies and Applications in Cell-Free Synthetic Biology

Challenges and Opportunities

Summary

Acknowledgments

References

Chapter 16. Towards Engineered Light–Energy Conversion in Nonphotosynthetic Microorganisms

Introduction

Incorporation of Simple Light-Driven Proton Pumps Into Engineered Microorganisms

Increasing the Complexity and Efficiency of Light-Energy Capture and Conversion

Combining Light-Energy Conversion and CO2 Fixation

From Biological to Artificial Photosynthetic Systems

Future Directions

References

Chapter 17. Applications of Engineered Synthetic Ecosystems

Introduction

Targeting Microbial Communities for Forward Engineering

Towards Synthetic Community Engineering

Future Prospects for Synthetic Ecosystems

Acknowledgments

References

Index