Metabolic Engineering in the Post Genomic Era
Publisher: Horizon Bioscience
Editors: Boris N. Kholodenko Thomas Jefferson University, Philadelphia, PA 19107, USA
and Hans V. Westerhoff BioCentrum Amsterdam, Free University, NL-1081 HV Amsterdam, The Netherlands
Publication date: January 2004
ISBN-10: 0-9545232-2-9
ISBN-13: 978-0-9545232-2-0
Pages: ix plus 456
Engineering living cells continues to pose immense challenges to the researcher. In fact many bioengineers have only just started to appreciate the full extent of the hierarchical control used by living systems: upon attempts to increase the activity of a "rate-limiting" step, the multiple feedbacks at the metabolic, signaling and genetic levels result in the rate-limiting step shifting to elsewhere in that pathway or even to elsewhere in the whole organism. The advent of full-force genomics should enable preventing this response, however, it has been difficult for researchers to know where to turn for guidance. This book aims to help the reader understand and deal with the plasticity of living cell factories and to turn the plasticity into the desired rather than the adverse direction. The book brings together all the recent, most important breakthroughs in this exciting field: Internationally renowned key scientists have reviewed each topic in detail. In the Introduction, the editors give an overview of new approaches and spell out what the engineer and the industry may now really begin to aim for; they even adapt the definition of metabolic engineering to befit the post-genomics era. Other topics included are: the experimental approaches necessary to understand cellular regulation at all of its hierarchical levels, including proteomics [Chapter 2], metabolomics [Chapter 3] and fluxomics [Chapter 4]; new tools that help metabolic engineering [Chapters 5-7]; modeling of living cells, e.g. finding metabolic pathways [Chapter 8] and comparing the actual and predicted use of these in living organisms such as E. coli and Corynebacteria [Chapters 9, 10]; the optimization of cell factories as production organisms (e.g., use of whole cell models, silicon cells, and coordinate manipulation of multiple genes [Chapters 12-15]). A chapter on future perspectives directs further developments of the field in the near future.
Essential reading for everyone with an interest in engineering living cells including: Metabolic engineers, bioengineers, biotechnologists, molecular biologists, and pharmaceutical and biotechnology companies.
Key Features:
* Detailed Discussions of Cutting Edge Topics
* Expert International Authors
* Fully Up-To-Date
* Broad Coverage
* Future Perspectives
* Useful Index
Reviews:
"This book is an excellent collection of reviews by many of the key players." from Microbiology Today (2004) 31: 101.
"Among the excellent chapters I should like to mention Stefan Schuster's account of metabolic pathway analysis ... other good chapters include accounts of magnetic resonance methods (Kevin Brindle), analysis of regulatory strengths in networks (Pedro Mendes and others), use of databases (Peter Karp), mathematical modelling (Wolfgang Wiechert and Ralf Takors). ... some of these are individually excellent ..." from The Biochemist (June 2004).
Chapter List:
Introduction
Chapter 1: Metabolic Engineering, What it Was and What it is
Hans V. Westerhoff and Boris N. Kholodenko
Analytic Tools
Chapter 2: Proteomics in Metabolic Engineering
Anders Blomberg
Chapter 3: Magnetic Resonance Spectroscopy and Imaging - Powerful Tools for Functional Genomics
Kevin M. Brindle
Chapter 4: Metabolic Flux Analysis in the Post Genomic Era
Margarida Moreira dos Santos, Mats Åkesson and Jens Nielsen
Chapter 5: Regulatory Strength Analysis for Inferring Gene Networks
Alberto de la Fuente, Paul Brazhnik and Pedro Mendes
Engineering Tools
Chapter 6: The MetaCyc Metabolic Pathway Database
Peter D. Karp
Chapter 7: Experimental Modulation of Gene Expression
Brian J. Koebmann, Jens Tornøe, Björn Johansson and Peter R. Jensen
Modeling Methodology
Chapter 8: Metabolic Pathway Analysis in Biotechnology
Stefan Schuster
Chapter 9: In Silico Cells: Studying Genotype-Phenotype Relationships Using Constraints-Based Models
Jason A. Papin, Nathan D. Price and Bernhard Ø. Palsson
Chapter 10: A Multi-scale Approach for the Predictive Modeling of Metabolic Regulation
Sören Petersen, Eric von Lieres, Albert A. de Graaf, Hermann Sahm and Wolfgang Wiechert
Chapter 11: Validation of Metabolic Models: Concepts, Tools, and Problems
Wolfgang Wiechert
Examples of Applications
Chapter 12: Applications of Whole Cell and Large Pathway Mathematical Models in the
Pharmaceutical Industry
Igor Goryanin, Oleg Demin and Frank Tobin
Chapter 13: Metabolic Engineering of Branched Systems: Redirecting the Main Pathway Flux
Jacky L. Snoep, Marcel H. N. Hoefnagel and Hans V. Westerhoff
Chapter 14: Redirecting Metabolism by Co-ordinate Manipulation of Multiple Genes
Claire Halpin and Martin Ryan
Chapter 15: Metabolic Engineering and Flux Analysis of Glycine Betaine Synthesis in Plants: Progress and Prospects
David Rhodes, Scott D. McNeil, Michael L. Nuccio and Andrew D. Hanson
Perspectives
Chapter 16: Metabolic Engineering in the Post Genomic Era: What it Should Become
Hans V. Westerhoff and Boris N. Kholodenko