Book review: Systems Metabolic Engineering

Authors


Abstract

original image

Systems Metabolic Enginering, edited by Christoph Wittmann and Sang Yup Lee “sits at the crossroads of being an introductory book providing an overview of the field and a handy desk-reference for state-of-the-art case studies for the expert metabolic engineer”. Read this book review by Hal Alper.

Systems Metabolic Engineering by Christoph Wittmann and Sang Yup Lee (Editors), Springer, 2012, 387 pages. ISBN 978-94-007-4534-6

Prof. Hal S. Alper halper@che.utexas.edu*, * Department of Chemical Engineering, Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX, USA

original image

The field of systems metabolic engineering aims to merge traditional metabolic engineering paradigms with a systems-level understanding of cellular function [1, 2]. This capacity has empowered metabolic engineers to rapidly produce a plethora of new molecules in cellular systems [3]. In this vain, it is timely that Christoph Wittmann and Sang Yup Lee have co-edited a contributed book titled “Systems Metabolic Engineering” recently published by Springer. Both Christoph and Sang Yup are pioneers in the field of systems metabolic engineering and together, they have compiled a contemporary overview of the field. This eleven-chapter book is individually authored by prominent names in the field. The book starts with several chapters that highlight essential tools of systems metabolic engineering and concludes with several vignettes in the form of case studies across six distinct organisms/cell types. The book sits at the crossroads of being an introductory book providing an overview of the field and a handy desk-reference for state-of-the-art case studies for the expert metabolic engineer.

The book starts with four chapters highlighting fundamentals of genome-scale models (Chapter 1), the development of kinetic models of metabolism (Chapter 2), omics technologies along with a case study of comparative omics (Chapter 3), and an overview of synthetic biology approaches and DNA assembly technologies (Chapter 4). These chapters are written by experts in the field including Bernhard Palsson, Sang Yup Lee, Hiroshi Shimizu, and Sven Panke. While these chapters all provide a great fundamental overview of technologies in the field, I would have personally started the book with the omics chapter as it forms the basis for the data input needed in genome-scale metabolic modeling. Chapter 2 is a comprehensive chapter that provides in-depth derivations for basic metabolic modeling. I particularly like how this chapter starts from fundamentals of reaction kinetics and builds toward large-scale models and data-fitting. I will certainly be pointing people in the field to this chapter to learn about the fundamentals of metabolic modeling. In this regard, I feel that a novice to the field would prefer to see Chapter 2 before Chapter 1, as Chapter 1 jumps quickly into terminology and assumes an implicit understanding of stoichiometric modeling. Nonetheless, the content of these chapters is contemporary and comprehensive and provides a great state-of-the-art overview of tools and methodologies for systems metabolic engineering.

The second part of the book focuses on individual case-studies sorted by cell type, including Escherichia coli (Chapter 5), Corynebacterium glutamicum (Chapter 6), Clostridium acetobutylicum (Chapter 7), Penicillium chrysogenum (Chapter 8), Saccharomyces cerevisiae (Chapters 9 and 10), and mammalian cell systems (Chapter 11). Once again, these chapters are authored by experts in the field, such as Sang Yup Lee, Christoph Wittmann, Terry Papoutsakis, Sef Heijnen, Jens Nielsen, Akihiko Kondo, and Greg Stephanopoulos. Since these chapters are each individually authored, they vary in scope and delivery. Some of these chapters provide a broad overview of many experiences related to engineering one organism (for example, Sang Yup highlights several of his triumphs in metabolically engineering E. coli to produce products from chemicals to fuels to pharmaceuticals in Chapter 5). Other chapters provide extensive detail and data for one particular phenotype of interest (such as Chapter 7, which discusses stress response and tolerance in C. acetobutylicum using a systems approach). Chapter 8 illustrates the significant amount of work involved to make large-scale, dynamic models and merge these models with the principles of metabolic control analysis. I tend to prefer the chapters with this latter flavor as this provides a detailed account of the trials-and-tribulations of systems metabolic engineering. This section concludes with a window into the future in Chapter 11 where systems level metabolic flux analysis meets cancer metabolism. Collectively, these chapters provide authoritative overviews that highlight success in both understanding and engineering organisms. These chapters also provide a great overview of the literature (with Chapter 9 having over 380 references cited). Thus, these chapters provide great overviews for novices in the field to obtain up-to-date information for their organism of choice. I particularly like how the editors opted to separate these case-studies by organism as it provides a logical intellectual breakdown.

Overall, Systems Metabolic Engineering edited by Christoph Wittmann and Sang Yup Lee provides an excellent, up-to-date overview of the field. They combine the expertise of many leading research groups across the world to deliver a compelling, authoritative discussion of systems metabolic engineering. This book will be an easy read for professors, researchers, and students. Moreover, this book contains the overview necessary for those new to the field, yet the detail and examples relevant to those who are long-time practitioners. In conclusion, this book is a must read for those interested in systems metabolic engineering.

Prof. Hal S. Alper

Department of Chemical Engineering, Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX, USA, E-mail: halper@che.utexas.edu

About the book editors

original image

Christoph Wittmann is Professor and Managing Director of the Institute of Biochemical Engineering at the Braunschweig University of Technology and a member of the Braunschweig Integrated Centre for Systems Biology and the Centre for Pharmaceutical Engineering. Prior to his current position, he received his PhD in biotechnology at the German Research Institute for Biotechnology (GBF) in Braunschweig, was Postdoc at the University of Helsinki, research group leader at the Biochemical Engineering Institute at Saarland University and Professor for Biotechnology at Münster University. He has published 100 journal papers and 10 book contributions. He holds 15 patents and patent applications, which are mainly in the area of metabolic engineering and industrial strain and process development. He has received the PhD award of the German Research Institute of Biotechnology and the Young Scientist Award of the European Federation of Biotechnology. His research interests comprise systems biology and biotechnology, fluxomics and metabolomics, systems metabolic engineering and industrial biotechnology with a focus on white (industrial) biotechnology.

original image

Sang Yup Lee is Distinguished Professor at the Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST). He has published 420 journal papers, 58 books/book chapters, and more than 550 patents. He has received numerous awards including National Order of Merit, Merck Metabolic Engineering Award from Merck, and many more. He is currently Fellow of AAAS, Fellow of American Academy of Microbiology, Fellow of Korean Academy of Science and Technology, Fellow of Society for Industrial Microbiology, Foreign Associate of National Academy of Engineering (USA), Chair of the Global Agenda Council on Biotechnology of World Economic Forum, and Co-Chair of the World Council on Industrial Biotechnology. Sang Yup is also dedicated to scientific advancement through his role as Editor-in-Chief of Biotechnology Journal, and Associate Editor and board member of numerous other journals. His research interests are systems biology and biotechnology, synthetic biology, industrial biotechnology, metabolic engineering, and nanobiotechnology.

Ancillary