Natural Product Biosynthesis by Microorganisms and Plants Part C

Natural Product Biosynthesis by Microorganisms and Plants Part C

1st Edition - November 1, 2012

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  • Editor: David Hopwood
  • eBook ISBN: 9780124046177
  • Hardcover ISBN: 9780124046344

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Description

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.

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

Readership

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

Table of Contents

  • 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

Product details

  • No. of pages: 512
  • Language: English
  • Copyright: © Academic Press 2012
  • Published: November 1, 2012
  • Imprint: Academic Press
  • eBook ISBN: 9780124046177
  • Hardcover ISBN: 9780124046344

About the Serial Volume Editor

David Hopwood

Affiliations and Expertise

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

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