Synthetic Biology of Yeasts: Tools and Applications

Preface
Contents
Synthetic Biology Tools and Cellular Engineering
1 Rational Metabolic Pathway Prediction and Design: Computational Tools and Their Applications for Yeast Systems and Synthetic Biology
1 Introduction
2 In Silico Pathway Prediction and Design
2.1 Data- and Knowledge-Bases for Metabolic Reaction Network Reconstruction
2.2 Pathway Prediction Using Retro-Biosynthesis Tools
2.3 Stoichiometry-Based Optimization Methods for Pathway (Re)design
3 Case Studies of Metabolic Pathway Prediction and Optimization in Yeast
3.1 Balancing Redox Cofactor Supply for Improving Substrate Utilization and Isoprenoids Production
3.2 Increasing Cytosolic Acetyl-CoA Availability for Metabolic Production
3.3 Engineering a Heterologous CBB Cycle for CO2 Fixation
4 Challenges and Outlook
2 Construction and Assembly of Standardized Biobricks for Synthetic Pathways Engineering in Yeasts
1 General Concept of Modularity
2 Historical Outline
3 Restriction Digestion/Recombination-Based Assembly Strategies
3.1 BioBricks
3.2 GoldenGate
3.3 Gateway
4 Overlap Assembly Strategies
4.1 Gibson
4.2 USER®
4.3 OE-PCR
5 Summary
3 Cellular Engineering of Yarrowia lipolytica for Biomanufacturing of High-Value Products from Oils and Fats
1 Introduction
2 Oils- or Fats-Substrate Utilization
3 CFD Modeling and Fermentation Engineering for Improving Biosynthesis from Oils and Fats
3.1 Investigation of Oil–Water Mixing in Stirred Bioreactor by CFD Simulation
3.2 Fermentation Engineering for Improved Biosynthesis from Oils and Fats
4 Cell Morphology Engineering in Dimorphic Yeast Y. lipolytica
4.1 Regulation of Yeast-To-Hyphal Transition in Y. lipolytica
4.2 The MAPK Pathway in Y. lipolytica
4.3 The cAMP-Dependent PKA Pathway in Y. lipolytica
4.4 Cell Morphology Engineering for Enhanced Utilization of Oils and Fats
5 Biosynthesis of Wax Esters from Oils and Fats
5.1 Characterization of the Wax Ester Biosynthesis Pathway
5.2 Introducing Wax Ester Biosynthesis Pathway into Yarrowia lipolytica
6 Transporter Engineering in Yeasts
6.1 Sugar Transport
6.2 Fatty Acid Transport
6.3 Product Export
7 Conclusions
4 Whole Cell Yeast-Based Biosensors
1 Introduction
2 Initial Technical Considerations
3 Analytes Suitable for Whole-Cell Yeast-Based Biosensors
4 Detection Systems for Whole-Cell Yeast-Based Biosensors
4.1 General Considerations
4.2 Detectors for Cytoplasmic Analytes
4.3 Detectors for Analytes that Remain Outside of Cells
5 Transduction and Amplification Pathways
5.1 Typical Transduction Pathways Used by Whole-Cell Yeast-Based Biosensors
5.2 Other Potentially Useful Transduction Pathways
5.3 Amplification
6 Response and Readout
6.1 Color-Based Reporters
6.2 Light-Based Reporters
6.3 Olfactory Reporters
6.4 Other Potentially Useful Reporters
7 Whole-Cell Biosensor Housing and Reading Devices
8 Long-Term Storage
9 Conclusions
Applications of Yeast Synthetic Biology
5 Yeast Synthetic Biology Approaches for the Production of Valuable Polyphenolic Compounds
1 Introduction
2 Polyphenolic Compounds
3 Biological Activities
3.1 Antioxidant
3.2 Anticancer
3.3 Antiviral
3.4 Anti-Inflammatory and Wound Healing Agents
4 Biosynthetic Pathway
5 Yeasts as Valuable Chassis
6 Case Studies: Production of Hydroxycinnamic Acids and Polyphenolic Compounds in Yeasts
6.1 Heterologous Production of Hydroxycinnamic Acids
6.2 Heterologous Production of Flavonoids
6.3 Heterologous Production of Stilbenoids
6.4 Heterologous Production of Coumarins
6.5 Heterologous Production of Curcuminoids
6.6 Heterologous Production of Polyphenolic Amides
7 Conclusions
6 Yeast Synthetic Biology for Production of Artemisinin as an Antimalarial Drug
1 Introduction
2 Importance of Terpenoids Production
3 Terpenoids Biosynthetic Pathway in Plants
3.1 MEP (Methylerythritol 4-Phosphate) Pathway Versus the MVA (Mevalonate) Pathway
3.2 Sesquiterpene Lactones
3.3 Artemisinin Biosynthetic Pathway in Artemisia annua
4 Application of Artemisinins in Medicine
4.1 Antimalarial
4.2 Anti-inflammation
4.3 Anticancer
4.4 Antiviral and Anti-SARS-CoV-2
5 Yeast Synthetic Biology for Artemisinin Precursors Production
5.1 Amorphadiene Production
5.2 Artemisinic Acid Production
6 Production of Artemisinin in planta Versus Application of Yeast SynBio
6.1 Metabolic Engineering of Artemisinin in Artemisia annua
6.2 In Planta Artemisinin Production
7 Conclusions
7 Yeast Synthetic Biology for the Production of Terpenoids Derived from Traditional Chinese Medicinal Plants
1 Introduction of Terpenoids and Their Production from Traditional Chinese Medicinal Plants
2 Terpenoid Biosynthesis Pathways in Nature
3 Identification of Key Genes Involved in Terpenoid Production from Traditional Chinese Medicinal Plants
4 Engineering Yeasts for the Production of Terpenoid Precursors
5 Production of Artemisinin Precursor of Artemisinic Acid Derived from Artemisia Annua in Yeasts
6 Production of Rare Ginsenosides Derived from Panax Plants in Yeasts
7 Production of Licorice Triterpenoid Derived from Glycyrrhiza Plants
8 Production of Other Terpenoids Derived from Traditional Chinese Medicinal Plants in Yeasts
9 Conclusion and Perspective
8 Application of Yeast Synthetic Biology for the Production of Citrus Flavors
1 Introduction
2 Natural Origin(s) of Valencene and Nootkatone
3 Yields of Valencene and Nootkatone in Native Hosts
4 Importance and Application of Valencene and Nootkatone
4.1 Flavor and Fragrance Industry
4.2 Therapeutic Benefits
5 Nootkatone and Valencene Biosynthetic Pathway in Native Hosts
6 Methods for Production of Valencene and Nootkatone
6.1 Extraction from Native Hosts
6.2 Chemical Synthesis
6.3 Biotransformation (or Bioconversion)
6.4 Application of Synthetic Biology Using Yeast Platforms
7 Conclusion
9 Synthesis of Polyols and Organic Acids by Wild-Type and Metabolically Engineered Yarrowia lipolytica Strains
1 Introduction
2 Yarrowia lipolytica
3 Organic Acid
3.1 Citric Acid
3.2 Iso-citric Acid
3.3 Succinic Acid
3.4 Itaconic Acid
3.5 α-ketoglutaric Acid
4 Polyols
4.1 Mannitol
4.2 Erythritol
4.3 Erythrulose
4.4 Threitol
5 Conclusion and Prospects
References
10 Recent Advances in Synthetic Biology Applications of Pichia Species
1 Introduction
2 Synthetic Biology Parts and Tools
2.1 Promoters and Terminators
2.2 Episomal Plasmids and Integration Plasmids
2.3 Genome Editing and Integration Loci
2.4 Commonly Used Strains
2.5 Signal Peptides for Mediating Protein Secretion
2.6 Co-expression of Chaperones to Facilitate Protein Folding
2.7 Cell Surface Display
3 Applications of P. pastoris in Biomanufacturing
3.1 Recombinant Proteins
3.2 Bulk Chemicals
3.3 Natural Products
4 Recent Advances in Engineering P. kudriavzeii
5 Conclusions and Perspectives
11 Kluyveromyces marxianus as a Platform in Synthetic Biology for the Production of Useful Materials
1 Introduction
2 Assimilation Capacity of Various Substrates
3 Thermotolerance and High-Temperature Fermentation Ability
4 Findings from Complete Genome Sequencing and Transcriptome Analysis
5 Possible Mechanism of Thermotolerance
6 High Protein Production Ability
7 High Ability of Non-homologous End-Joining for Genetic Engineering
8 Genome Editing Tools
9 Examples of Production of Other Useful Materials by  K. marxianus
9.1 Flavor Metabolites
9.2 Fructose
9.3 Xylitol Formation
10 Conclusions
12 Synthetic Biology in the Candida (CTG) Clade
1 Introduction
2 Taxonomy
3 Classical Genetic Tools
3.1 Selection Markers
3.2 Reporter Genes
3.3 Auto-replicating Sequence
3.4 Recombinases
3.5 Tetracycline-Regulatable Dual System
3.6 CRISPR–Cas9 System
4 Omics Resources
4.1 Genomics
4.2 Transcriptomics
4.3 Proteomics
4.4 Metabolomics
4.5 Fluxomics
5 Candida Metabolic Engineering
5.1 Ethanol Production
5.2 Lipid Production
5.3 Vitamin Production
5.4 Other Valuable Compound Bio-production
5.5 Bioremediation
5.6 Biocontrol
6 Concluding Remarks and Perspectives