Natural Product Biosynthesis by Microorganisms and Plants Part C

Natural Product Biosynthesis by Microorganisms and Plants Part C, 1st Edition

Natural Product Biosynthesis by Microorganisms and Plants Part C, 1st Edition,David Hopwood,ISBN9780124046344

Methods in Enzymology

D Hopwood   

Academic Press




229 X 152

This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field, covering natural product biosynthesis by microorganisms and plants.

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Key Features

  • This new volume continues the legacy of this premier serial
  • Contains quality chapters authored by leaders in the field
  • The third of 3 volumes, it has chapters on such topics as metabolic pathways in Aspergillus oryzae, heterologous gene clusters and cyanobacteria as a source of natural products


This new volume of Methods in Enzymology continues the legacy of this premier serial by containing quality chapters authored by leaders in the field. The third of 3 volumes covering Natural product biosynthesis by microorganisms and plants.


Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

David Hopwood

Affiliations and Expertise

John Innes Centre and AFRC Institute of Plant Science Research, Norwich, UK

View additional works by David A. Hopwood

Natural Product Biosynthesis by Microorganisms and Plants Part C, 1st Edition



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


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


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


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


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


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


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


Chapter Eight. Phylogenetic Approaches to Natural Product Structure Prediction

1 Introduction

2 Working with Sequence Data

3 NaPDoS

4 Conclusions and Future Directions


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


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


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


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


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


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


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


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


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


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


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

1 Persisters and Infectious Disease

2 Mechanisms of Persister Formation

3 Persister Eradication


Author Index

Subject Index

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