Natural Product Biosynthesis by Microorganisms and Plants Part C

Contributors

Preface

Methods in Enzymology

Chapter One. Methods for the Study of Endophytic Microorganisms from Traditional Chinese Medicine Plants

1 Introduction

2 Experimental Methods

3 Novel Bioactive Compounds from Endophytic Actinobacteria

4 Conclusion

References

Chapter Two. Cyanobacteria as a Source of Natural Products

1 Introduction

2 Cyanobacteria as Starting Material for Natural Products

3 Screening for New Compounds and Producers

4 Genomic Mining of Cyanobacterial Natural Products

5 Summary

References

Chapter Three. Isolating Antifungals from Fungus-Growing Ant Symbionts Using a Genome-Guided Chemistry Approach

1 Introduction

2 Strain Isolation and Genome Sequencing

3 Identifying Antifungals made by Pseudonocardia P1

4 Identifying Antifungals made by S. albus S4

5 Summary and Perspectives

References

Chapter Four. Gamma-Butyrolactone and Furan Signaling Systems in Streptomyces

1 Introduction

2 AfsA-Like Enzymes and the Biosynthesis of Signaling Molecules

3 Heterologous Expression of an AfsA-Like-Containing Mini-Cluster Combined with Comparative Metabolic Profiling

4 Genetic Disruption of mmfLHP and Chemical Complementation Experiments

5 Conclusion

References

Chapter Five. Old Meets New: Using Interspecies Interactions to Detect Secondary Metabolite Production in Actinomycetes

1 Introduction

2 Setting Up Binary Actinomycete Interactions

3 Activity-Guided Fractionation for Amychelin Isolation

4 Determining the Affinity of Amychelin for Fe

5 Identifying the Amychelin Biosynthetic Gene Cluster

6 Transcriptomic Analysis using Nanostring Technology

7 Summary

References

Chapter Six. Finding and Analyzing Plant Metabolic Gene Clusters

1 Introduction

2 Discovery of Plant Metabolic Gene Clusters Through Genetic Analysis

3 Mining Genomes for Secondary Metabolic Gene Clusters

4 Validating Candidate Metabolic Gene Clusters

5 Imaging Gene Clusters

6 Future Prospects

References

Chapter Seven. Genomic Approaches for Interrogating the Biochemistry of Medicinal Plant Species

1 Introduction

2 Plant Material Selection and Quality

3 Isolation of RNA

4 Generation of Next-Generation whole Transcriptome Sequences

5 Assembly of a Reference Transcriptome

6 Assessment of Expression Abundances

7 Summary

8 Useful Links

References

Chapter Eight. Phylogenetic Approaches to Natural Product Structure Prediction

1 Introduction

2 Working with Sequence Data

3 NaPDoS

4 Conclusions and Future Directions

References

Chapter Nine. Using a Virus-Derived System to Manipulate Plant Natural Product Biosynthetic Pathways

1 Introduction

2 Deleted Vectors Based on Cowpea Mosaic Virus

3 Expression of Enzymes in Plants Using pEAQ Vectors

4 Conclusions and Perspectives

References

Chapter Ten. DNA Assembler

1 Introduction

2 General Guidelines for Construct Design

3 Heterologous Expression and Fine Modification of Natural Product Gene Clusters

4 Characterization of Natural Product Gene Clusters

5 Construction of Artificial Gene Clusters

References

Chapter Eleven. Reassembly of Functionally Intact Environmental DNA-Derived Biosynthetic Gene Clusters

1 Introduction

2 Protocol for Constructing, Arraying, and Screening Environmental Libraries

3 Use of TAR to Reassemble Overlapping Clones into Complete Biosynthetic Pathways

4 Downstream Analysis

5 Example

References

Chapter Twelve. A Toolkit for Heterologous Expression of Metabolic Pathways in Aspergillus oryzae

1 Introduction

2 Fundamental Aspects of Vector Development

3 Heterologous Expression of a Fungal Natural Product Pathway in A.oryzae

4 Methods

5 Summary

References

Chapter Thirteen. De Novo Synthesis of High-Value Plant Sesquiterpenoids in Yeast

1 Introduction

2 Yeast Culture and Metabolite Analysis

3 Expression Plasmid Construct and Transformation

4 De Novo Production of Sesquiterpenes

5 De Novo Production of Hydroxylated Sesquiterpene

6 General Discussion

References

Chapter Fourteen. Streptomyces coelicolor as an Expression Host for Heterologous Gene Clusters

1 Introduction

2 S. coelicolor Strains for Heterologous Expression

3 Cloning of Secondary Metabolite Gene Clusters

4 Introduction and Propagation of Cloned Gene Clusters in S. coelicolor Hosts

5 Preservation of Selected Clones

6 Growth in Liquid Culture for Metabolite Analysis

7 Comparative Metabolic Profiling

References

Chapter Fifteen. Toward Awakening Cryptic Secondary Metabolite Gene Clusters in Filamentous Fungi

1 Introduction

2 Activation Handles of Fungal Secondary Metabolite Gene Clusters

3 Mining for Novel Compounds and Their Biosynthetic Genes

4 Genetic Manipulation of Biosynthetic and Regulatory Genes

5 Secondary Metabolite Analysis

References

Chapter Sixteen. Regulatory Cross Talk and Microbial Induction of Fungal Secondary Metabolite Gene Clusters

1 Introduction

2 Production of Secondary Metabolites by Overexpression of Pathway-Specific Regulatory Genes

3 Genetic Manipulation of Signal Transduction Cascades

4 Microbial Induction of Fungal Secondary Metabolite Gene Clusters

References

Chapter Seventeen. Waking up Streptomyces Secondary Metabolism by Constitutive Expression of Activators or Genetic Disruption of Repressors

1 Introduction

2 Awakening Cryptic Gene Clusters with Pathway-Specific Activators

3 Awakening Cryptic Gene Clusters Using Transcriptional Repressor Disruptions

4 Comparative Metabolic Profiling to Identify Novel Metabolites in the Engineered Strains

5 Conclusion/Perspectives

References

Chapter Eighteen. Use and Discovery of Chemical Elicitors That Stimulate Biosynthetic Gene Clusters in Streptomyces Bacteria

1 Introduction

2 Role of HDAC-Like Acetyltransferases in Controlling the Expression of Biosynthetic Pathways

3 Use of HDAC Inhibitors to Stimulate Expression of Secondary Metabolic Genes

4 Screening for HDAC Inhibitors from Streptomyces Bacteria

5 Conclusion

References

Chapter Nineteen. Persister Eradication: Lessons from the World of Natural Products

1 Persisters and Infectious Disease

2 Mechanisms of Persister Formation

3 Persister Eradication

References

Author Index

Subject Index