The Metabolic Pathway Engineering Handbook, Two Volume Set  book cover
1st Edition

The Metabolic Pathway Engineering Handbook, Two Volume Set

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ISBN 9780849339233
Published August 18, 2009 by CRC Press
1259 Pages 250 B/W Illustrations

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Book Description

Christina Smolke, who recently developed a novel way to churn out large quantities of drugs from genetically modified brewer’s yeast, is regarded as one of the most brilliant minds in biomedical engineering. In this handbook, she brings together pioneering scientists from dozens of disciplines to provide a complete record of accomplishment in metabolic pathway engineering. With a wealth of cutting edge research and analysis, this work also serves as an invaluable resource for those seeking to add their own contributions. Organized by topic, this 3000 page reference is available as two volumes that can be purchased individually or as a set.


The first volume provides an overview of metabolic pathway engineering with a look towards the future. It discusses cellular metabolism, including transport processes inside the cell and energy generating reactions, as well as rare metabolic conversions. This volume also explores balances and reaction models, the regulation of metabolic pathways, and genome scale and multiscale modeling tools. It also covers developing appropriate hosts for metabolic engineering including the use of Escherichia coli, yeast, Bacillus subtilis, Streptomyces, filamentous fungi, annd mammalian cells using cell culture.

Tool and Applications

The second volume delves into evolutionary tools, including those associated with gene expression for metabolic pathway engineering. It covers applications of emerging technologies, including research on genome-wide technologies, DNA and phenotypic microarrays, and proteomics tools for experimentally determining flux through pathways. It also evaluates emerging applications for producing fine chemicals, drugs, and alternative fuels.

Table of Contents

Volume I

Introduction and Preface to Handbook, Christina D. Smolke

Progression of biological synthesis methods towards commercial relevance

The field of metabolic engineering

An overview of the metabolic pathway engineering handbook

Metabolic engineering: looking towards the future

Section I. Cellular Metabolism, Vincent Martin

Transport processes inside the cell

Energy generating reactions

Biosynthesis of important building blocks

Polymerization of building blocks to macromolecules

Rare metabolic conversions – harvesting diversity through nature

Section II. Balances and Reaction Models, Walter van Gulik

Growth nutrients and diversity

Mass balances, rates, and experiments

Data reconciliation and error detection

Black box models for growth and product formation

Metabolic models for growth and product formation

A thermodynamic description of microbial growth

Section III. Regulation of Metabolic Pathways, James Liao

Regulation of specific pathways

Regulating of secondary metabolism

Building networks as assemblies of simpler control schemes

Section IV. Modeling Tools for Metabolic Engineering, Costas Maranas

Metabolic flux analysis

Metabolic control analysis

Structure and flux analysis of metabolic networks

Constraint-based genome-scale models of cellular metabolism

Multi-scale modeling of metabolic regulation

Validation of metabolic models

Section V. Developing Appropriate Hosts for Metabolic Engineering, Jens Nielsen

Escherichia coli as a well-developed host for metabolic engineering

Metabolic engineering in yeast

Metabolic engineering in Bacillus subtilis

Metabolic engineering in Streptomyces

Metabolic engineering in filamentous fungi

Metabolic engineering in mammalian cells using cell culture


Volume II

Section VI. Evolutionary Tools in Metabolic Engineering, Claudia Schmidt-Dannert

Evolutionary engineering of industrially important microbial phenotypes

Expanding enzyme function and activity through molecular evolution

Evolving the function of DNA and RNA regulatory regions through molecular evolution

Evolving pathways and genomes for the production of natural and novel compounds

Models predicting optimized evolutionary strategies

Section VII. Gene Expression Tools for Metabolic Pathway Engineering, Christina Smolke

Low-copy number plasmids as artificial chromosomes

Chromosomal engineering strategies

Regulating gene expression through engineered RNA technologies

Tools designed to regulate translational efficiency

Regulating gene expression through post-translational modifications

Engineering bifunctional enzymes for optimized metabolite transfer between sequential conversion steps

Practical pathway engineering – demonstration in integrating tools

Section VIII. Applications of Emerging Technologies to Metabolic Engineering, Jay Keasling

Genome-wide technologies: DNA and phenotypic microarrays, proteomics

Monitoring and measuring the metabolome

Section IX. Future Prospects in Metabolic Engineering, Bernhard Palsson and Sang Yup Lee

Genome-scale models, systems biology, and metabolic engineering

Cell-free systems for metabolic engineering

Dynamic in silico cell models

Appendix I: Tools for Experimentally Determining Flux through Pathways, Ralf Takors

Measuring flux by isotope labeling

Tools for measuring intermediate and product formation

Quantitative analysis of labeling data

Appendix II: Applications, Brian Pfleger and Brian Brazeau

Cofactor regulation in biocatalytic redox reactions

Metabolic engineering for fine chemical production

Metabolic engineering for drug production

Metabolic engineering for alternative fuels


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